From b834a65c057cad6c7467ae28c087a6c3d31dae2e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Luk=C3=A1=C5=A1=20Krup=C4=8D=C3=ADk?= <lukas.krupcik@vsb.cz>
Date: Wed, 3 Aug 2016 11:40:39 +0200
Subject: [PATCH] version 0.4
---
README.md | 11 +-
.../outgoing-connections.md | 24 +-
.../shell-and-data-access.md | 24 +-
.../accessing-the-cluster/vpn-access.md | 26 +-
.../compute-nodes.md | 109 ++++++-
.../environment-and-modules.md | 14 +-
.../hardware-overview.md | 22 +-
.../introduction.md | 16 +-
.../anselm-cluster-documentation/network.md | 18 +-
.../anselm-cluster-documentation/prace.md | 42 ++-
.../remote-visualization.md | 35 ++-
.../capacity-computing.md | 8 +
.../introduction.md | 14 +-
.../job-priority.md | 10 +
.../job-submission-and-execution.md | 38 ++-
.../resources-allocation-policy.md | 26 +-
.../software/ansys.md | 12 +-
.../software/ansys/ansys-cfx.md | 10 +-
.../software/ansys/ansys-fluent.md | 18 +-
.../software/ansys/ansys-ls-dyna.md | 12 +-
.../software/ansys/ansys-mechanical-apdl.md | 10 +-
.../software/ansys/ls-dyna.md | 8 +
.../software/chemistry/molpro.md | 16 +-
.../software/chemistry/nwchem.md | 14 +
.../software/compilers.md | 16 +-
.../software/comsol/comsol-multiphysics.md | 46 +--
.../software/debuggers.md | 10 +
.../software/debuggers/allinea-ddt.md | 16 +-
.../debuggers/allinea-performance-reports.md | 16 +
.../software/debuggers/cube.md | 14 +
.../intel-performance-counter-monitor.md | 14 +-
.../debuggers/intel-vtune-amplifier.md | 18 +-
.../software/debuggers/papi.md | 20 +-
.../software/debuggers/scalasca.md | 10 +
.../software/debuggers/score-p.md | 13 +-
.../software/debuggers/summary.md | 12 +
.../software/debuggers/total-view.md | 26 +-
.../software/debuggers/valgrind.md | 22 +-
.../software/debuggers/vampir.md | 10 +
.../software/gpi2.md | 12 +
.../software/intel-suite.md | 10 +
.../software/intel-suite/intel-compilers.md | 10 +
.../software/intel-suite/intel-debugger.md | 14 +-
...intel-integrated-performance-primitives.md | 10 +
.../software/intel-suite/intel-mkl.md | 12 +-
.../intel-parallel-studio-introduction.md | 10 +
.../software/intel-suite/intel-tbb.md | 10 +
.../software/intel-xeon-phi.md | 30 +-
.../software/isv_licenses.md | 18 +-
.../software/java.md | 14 +
.../software/kvirtualization.md | 50 ++--
.../software/mpi-1/Running_OpenMPI.md | 10 +
.../software/mpi-1/mpi.md | 18 +-
.../software/mpi-1/mpi4py-mpi-for-python.md | 14 +
.../software/mpi-1/running-mpich2.md | 12 +-
.../numerical-languages/copy_of_matlab.md | 18 +-
.../numerical-languages/introduction.md | 16 +-
.../software/numerical-languages/matlab.md | 16 +-
.../software/numerical-languages/octave.md | 10 +
.../software/numerical-languages/r.md | 23 +-
.../software/numerical-libraries/fftw.md | 16 +
.../software/numerical-libraries/gsl.md | 15 +
.../software/numerical-libraries/hdf5.md | 30 +-
.../intel-numerical-libraries.md | 12 +
.../magma-for-intel-xeon-phi.md | 16 +
.../software/numerical-libraries/petsc.md | 18 +-
.../software/numerical-libraries/trilinos.md | 14 +-
.../software/nvidia-cuda.md | 16 +-
.../diagnostic-component-team.md | 31 +-
.../software/omics-master-1/overview.md | 211 +++++++------
.../priorization-component-bierapp.md | 23 +-
.../software/openfoam.md | 58 +++-
.../software/operating-system.md | 14 +
.../software/paraview.md | 14 +
.../storage-1/cesnet-data-storage.md | 26 +-
.../storage-1/storage.md | 54 ++--
.../cygwin-and-x11-forwarding.md | 18 +-
.../graphical-user-interface.md | 14 +-
.../graphical-user-interface/vnc.md | 28 +-
.../graphical-user-interface/vpnuiV.png | Bin 49733 -> 0 bytes
.../x-window-system.md | 12 +-
.../accessing-the-clusters/introduction.md | 22 +-
.../introduction.md | 18 +-
.../shell-access-and-data-transfer/pageant.md | 14 +-
.../shell-access-and-data-transfer/putty.md | 26 +-
.../puttygen.md | 26 +-
.../ssh-keys.md | 18 +-
.../vpn-connection-fail-in-win-8.1.md | 16 +-
.../applying-for-resources.md | 16 +-
.../introduction.md | 13 +-
.../certificates-faq.md | 29 +-
.../obtaining-login-credentials.md | 42 ++-
converted/docs.it4i.cz/index.md | 14 +-
.../salomon/accessing-the-cluster.md | 24 +-
.../outgoing-connections.md | 20 +-
.../accessing-the-cluster/vpn-access.md | 18 +-
.../salomon/environment-and-modules.md | 14 +-
.../hardware-overview-1/hardware-overview.md | 15 +-
converted/docs.it4i.cz/salomon/index.md | 21 +-
.../docs.it4i.cz/salomon/introduction.md | 15 +-
.../network-1/7d-enhanced-hypercube.md | 14 +-
.../network-1/ib-single-plane-topology.md | 15 +-
.../docs.it4i.cz/salomon/network-1/network.md | 15 +-
converted/docs.it4i.cz/salomon/prace.md | 47 +--
.../capacity-computing.md | 8 +
.../introduction.md | 16 +-
.../job-priority.md | 15 +-
.../job-submission-and-execution.md | 44 ++-
.../resources-allocation-policy.md | 30 +-
.../salomon/software/ansys/ansys-cfx.md | 11 +-
.../salomon/software/ansys/ansys-fluent.md | 20 +-
.../salomon/software/ansys/ansys-ls-dyna.md | 13 +-
.../software/ansys/ansys-mechanical-apdl.md | 11 +-
...ys-products-mechanical-fluent-cfx-mapdl.md | 9 +
.../salomon/software/ansys/ansys.md | 8 +
.../salomon/software/ansys/licensing.md | 12 +
.../ansys/setting-license-preferences.md | 17 +-
.../salomon/software/ansys/workbench.md | 9 +
.../salomon/software/chemistry/molpro.md | 14 +-
.../salomon/software/chemistry/nwchem.md | 12 +
.../salomon/software/chemistry/phono3py.md | 16 +
.../salomon/software/compilers.md | 14 +-
.../software/comsol/comsol-multiphysics.md | 47 +--
.../licensing-and-available-versions.md | 14 +-
.../salomon/software/debuggers.md | 10 +-
.../salomon/software/debuggers/aislinn.md | 22 +-
.../salomon/software/debuggers/allinea-ddt.md | 24 +-
.../debuggers/allinea-performance-reports.md | 15 +
.../debuggers/intel-vtune-amplifier.md | 17 +-
.../salomon/software/debuggers/report.png | Bin 0 -> 66893 bytes
.../salomon/software/debuggers/summary.md | 10 +-
.../salomon/software/debuggers/total-view.md | 27 +-
.../salomon/software/debuggers/valgrind.md | 18 +-
.../salomon/software/debuggers/vampir.md | 10 +-
.../software/intel-suite/intel-advisor.md | 8 +
.../software/intel-suite/intel-compilers.md | 8 +
.../software/intel-suite/intel-debugger.md | 18 +-
.../software/intel-suite/intel-inspector.md | 8 +
...intel-integrated-performance-primitives.md | 8 +
.../salomon/software/intel-suite/intel-mkl.md | 10 +-
.../intel-parallel-studio-introduction.md | 10 +-
.../salomon/software/intel-suite/intel-tbb.md | 8 +
.../intel-trace-analyzer-and-collector.md | 10 +-
.../salomon/software/intel-xeon-phi.md | 34 ++-
.../docs.it4i.cz/salomon/software/java.md | 12 +
.../salomon/software/mpi-1/Running_OpenMPI.md | 8 +
.../salomon/software/mpi-1/mpi.md | 16 +-
.../software/mpi-1/mpi4py-mpi-for-python.md | 12 +
.../numerical-languages/introduction.md | 14 +-
.../software/numerical-languages/matlab.md | 16 +-
.../software/numerical-languages/octave.md | 8 +
.../salomon/software/numerical-languages/r.md | 30 +-
.../salomon/software/operating-system.md | 12 +
.../salomon/storage/cesnet-data-storage.md | 26 +-
.../docs.it4i.cz/salomon/storage/storage.md | 48 ++-
html_md.sh | 218 +++++---------
source/exceptions_filter_auto | 18 --
source/{list_folder.txt => list_folder} | 0
source/list_image_mv | 98 ++++++
source/list_image_mv.txt | 9 +-
source/{list_md_mv.txt => list_md_mv} | 0
source/list_rm | 100 +++++++
source/list_rm.txt | 38 ---
source/repairIMG | 108 +++++++
source/replace | 148 +++++++++
source/replace.txt | 280 ------------------
166 files changed, 3031 insertions(+), 1052 deletions(-)
delete mode 100644 converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vpnuiV.png
create mode 100644 converted/docs.it4i.cz/salomon/software/debuggers/report.png
delete mode 100644 source/exceptions_filter_auto
rename source/{list_folder.txt => list_folder} (100%)
create mode 100644 source/list_image_mv
rename source/{list_md_mv.txt => list_md_mv} (100%)
create mode 100644 source/list_rm
delete mode 100644 source/list_rm.txt
create mode 100644 source/repairIMG
create mode 100644 source/replace
delete mode 100644 source/replace.txt
diff --git a/README.md b/README.md
index 5842d66f..9cd2312d 100755
--- a/README.md
+++ b/README.md
@@ -1,4 +1,4 @@
-Převod html dokumentace do md formátu (version 0.36) - BETA
+Převod html dokumentace do md formátu (version 0.4) - BETA
===========================================================
Výsledkem projektu by měl být skript pro stažení a převod stávající dokumentace na docs.it4i.cz do md formátu
@@ -18,11 +18,12 @@ Pro svou práci si naklonujete Gitem repozitář do svého pracovního adresář
> * interní a externí odkazy
> * formátování tabulek
> * formátovámí textu v některých místech
+> * doba převodu ~24min
>**Změny v nové verzi**
->* oprava odkazu na obrázky
->* vylepšené filtrování
->* přidání testovacího parametru t1 pro kontrolu změn, v následující verzi bude sloučen...
+> * oprava odkazu na obrázky a vylepšené filtrování
+> * přehled o počtu souboru a stavu převodu
+> * optimalizace, začlenění testovacích funkcí do hlavní větve programu
### Funkce skriptu
@@ -42,4 +43,4 @@ Testování
```bash
html_md.sh -t
-```
\ No newline at end of file
+```
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/outgoing-connections.md b/converted/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/outgoing-connections.md
index 342fc28f..77868ae9 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/outgoing-connections.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/outgoing-connections.md
@@ -5,6 +5,14 @@ Outgoing connections
+
+
+
+
+
+
+
+
Connection restrictions
-----------------------
@@ -44,7 +52,7 @@ local $ ssh -R 6000:remote.host.com:1234 anselm.it4i.cz
```
In this example, we establish port forwarding between port 6000 on
-Anselm and port 1234 on the remote.host.com. By ing
+Anselm and port 1234 on the remote.host.com. By accessing
localhost:6000 on Anselm, an application will see response of
remote.host.com:1234. The traffic will run via users local workstation.
@@ -55,7 +63,7 @@ Remote radio button. Insert 6000 to Source port textbox. Insert
remote.host.com:1234. Click Add button, then Open.
Port forwarding may be established directly to the remote host. However,
-this requires that user has ssh to remote.host.com
+this requires that user has ssh access to remote.host.com
```
$ ssh -L 6000:localhost:1234 remote.host.com
@@ -66,7 +74,7 @@ Note: Port number 6000 is chosen as an example only. Pick any free port.
### Port forwarding from compute nodes
Remote port forwarding from compute nodes allows applications running on
-the compute nodes to hosts outside Anselm Cluster.
+the compute nodes to access hosts outside Anselm Cluster.
First, establish the remote port forwarding form the login node, as
[described
@@ -80,7 +88,7 @@ $ ssh -TN -f -L 6000:localhost:6000 login1
```
In this example, we assume that port forwarding from login1:6000 to
-remote.host.com:1234 has been established beforehand. By ing
+remote.host.com:1234 has been established beforehand. By accessing
localhost:6000, an application running on a compute node will see
response of remote.host.com:1234
@@ -90,7 +98,7 @@ Port forwarding is static, each single port is mapped to a particular
port on remote host. Connection to other remote host, requires new
forward.
-Applications with inbuilt proxy support, experience unlimited to
+Applications with inbuilt proxy support, experience unlimited access to
remote hosts, via single proxy server.
To establish local proxy server on your workstation, install and run
@@ -114,6 +122,10 @@ local $ ssh -R 6000:localhost:1080 anselm.it4i.cz
```
Now, configure the applications proxy settings to **localhost:6000**.
-Use port forwarding to the [proxy server from compute
+Use port forwarding to access the [proxy server from compute
nodes](outgoing-connections.html#port-forwarding-from-compute-nodes)
as well .
+
+
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/shell-and-data-access/shell-and-data-access.md b/converted/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/shell-and-data-access/shell-and-data-access.md
index 82f3ae41..8bcf8a55 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/shell-and-data-access/shell-and-data-access.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/shell-and-data-access/shell-and-data-access.md
@@ -1,14 +1,22 @@
-Shell and data transfer
+Shell access and data transfer
==============================
+
+
+
+
+
+
+
+
Interactive Login
-----------------
-The Anselm cluster is ed by SSH protocol via login nodes login1
+The Anselm cluster is accessed by SSH protocol via login nodes login1
and login2 at address anselm.it4i.cz. The login nodes may be addressed
specifically, by prepending the login node name to the address.
@@ -19,7 +27,7 @@ login1.anselm.it4i.cz 22 ssh login1
login2.anselm.it4i.cz 22 ssh login2
The authentication is by the [private
-key](../../../get-started-with-it4innovations/ing-the-clusters/shell-access-and-data-transfer/ssh-keys.html)
+key](../../../get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.html)
Please verify SSH fingerprints during the first logon. They are
identical on all login nodes:
@@ -44,7 +52,7 @@ local $ chmod 600 /path/to/id_rsa
```
On **Windows**, use [PuTTY ssh
-client](../../../get-started-with-it4innovations/ing-the-clusters/shell-access-and-data-transfer/putty/putty.html).
+client](../../../get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/putty.html).
After logging in, you will see the command prompt:
@@ -79,10 +87,10 @@ Address Port
anselm.it4i.cz 22 scp, sftp
login1.anselm.it4i.cz 22 scp, sftp
login2.anselm.it4i.cz 22 scp, sftp
- class="discreet">dm1.anselm.it4i.cz class="discreet">22 class="discreet">scp, sftp</span>
+ class="discreet">dm1.anselm.it4i.cz 22 class="discreet">scp, sftp</span>
The authentication is by the [private
-key](../../../get-started-with-it4innovations/ing-the-clusters/shell-access-and-data-transfer/ssh-keys.html)
+key](../../../get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.html)
Data transfer rates up to **160MB/s** can be achieved with scp or sftp.
1TB may be transferred in 1:50h.
@@ -138,3 +146,7 @@ way to mount the Anselm filesystems directly as an external disc.
More information about the shared file systems is available
[here](../../storage.html).
+
+
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/vpn-access.md b/converted/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/vpn-access.md
index e245539b..99df6595 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/vpn-access.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/vpn-access.md
@@ -5,6 +5,14 @@ VPN Access
+
+
+
+
+
+
+
+
Accessing IT4Innovations internal resources via VPN
---------------------------------------------------
@@ -46,9 +54,9 @@ for automatic installation.
-](../executionaccess.jpg/@@images/4d6e7cb7-9aa7-419c-9583-6dfd92b2c015.jpeg "Execution access")
-
-
+access](../executionaccess.jpg/@@images/4d6e7cb7-9aa7-419c-9583-6dfd92b2c015.jpeg "Execution access")
+access
+
After successful installation, VPN connection will be established and
you can use available resources from IT4I network.
@@ -92,13 +100,13 @@ After a successful login, the client will minimize to the system tray.
If everything works, you can see a lock in the Cisco tray icon.
-connection](../anyconnecticon.jpg "Successfull connection")
+
If you right-click on this icon, you will see a context menu in which
you can control the VPN connection.
-
+
+
When you connect to the VPN for the first time, the client downloads the
profile and creates a new item "ANSELM" in the connection list. For
@@ -110,7 +118,7 @@ but just select the corresponding item.
Then AnyConnect automatically proceeds like in the case of first logon.
-
+
After a successful logon, you can see a green circle with a tick mark on
the lock icon.
@@ -120,3 +128,7 @@ the lock icon.
For disconnecting, right-click on the AnyConnect client icon in the
system tray and select **VPN Disconnect**.
+
+
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/compute-nodes.md b/converted/docs.it4i.cz/anselm-cluster-documentation/compute-nodes.md
index 46675a07..ae39e5e7 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/compute-nodes.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/compute-nodes.md
@@ -5,6 +5,14 @@ Compute Nodes
+
+
+
+
+
+
+
+
Nodes Configuration
-------------------
@@ -192,7 +200,7 @@ nodes.****
-**
+
**Figure Anselm bullx B510 servers****
@@ -207,17 +215,37 @@ Fat compute nodes 2 cn[208-209] 512GB 16 @ 2.4GHz qfat,
+
+
+
+
Processor Architecture
----------------------
+
+
+
+
Anselm is equipped with Intel Sandy Bridge processors Intel Xeon E5-2665
(nodes without accelerator and fat nodes) and Intel Xeon E5-2470 (nodes
with accelerator). Processors support Advanced Vector Extensions (AVX)
256-bit instruction set.
+
+
+
+
### Intel Sandy Bridge E5-2665 Processor
+
+
+
+
+
+
+
+
- eight-core
- speed: 2.4 GHz, up to 3.1 GHz using Turbo Boost Technology
- peak performance: 19.2 Gflop/s per
@@ -232,7 +260,23 @@ with accelerator). Processors support Advanced Vector Extensions (AVX)
- memory bandwidth at the level of the processor: 51.2 GB/s
+
+
+
+
+
+
+
+
### Intel Sandy Bridge E5-2470 Processor
+
+
+
+
+
+
+
+
- eight-core
- speed: 2.3 GHz, up to 3.1 GHz using Turbo Boost Technology
- peak performance: 18.4 Gflop/s per
@@ -262,8 +306,20 @@ $ qsub -A OPEN-0-0 -q qprod -l select=4:ncpus=16:cpu_freq=24 -I
```
+
+
+
+
In this example, we allocate 4 nodes, 16 cores at 2.4GHhz per node.
+
+
+
+
+
+
+
+
Intel Turbo Boost Technology is used by default, you can disable it for
all nodes of job by using resource attribute cpu_turbo_boost.
@@ -274,7 +330,19 @@ all nodes of job by using resource attribute cpu_turbo_boost.
Memory Architecture
-------------------
+
+
+
+
### Compute Node Without Accelerator
+
+
+
+
+
+
+
+
- 2 sockets
- Memory Controllers are integrated into processors.
@@ -288,7 +356,23 @@ Memory Architecture
- Populated memory: 8x 8GB DDR3 DIMM 1600Mhz
+
+
+
+
+
+
+
+
### Compute Node With GPU or MIC Accelerator
+
+
+
+
+
+
+
+
- 2 sockets
- Memory Controllers are integrated into processors.
@@ -302,7 +386,23 @@ Memory Architecture
- Populated memory: 6x 16GB DDR3 DIMM 1600Mhz
+
+
+
+
+
+
+
+
### Fat Compute Node
+
+
+
+
+
+
+
+
- 2 sockets
- Memory Controllers are integrated into processors.
@@ -318,3 +418,10 @@ Memory Architecture
+
+
+
+
+
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/environment-and-modules.md b/converted/docs.it4i.cz/anselm-cluster-documentation/environment-and-modules.md
index b4a02b88..c8ee979a 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/environment-and-modules.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/environment-and-modules.md
@@ -5,6 +5,14 @@ Environment and Modules
+
+
+
+
+
+
+
+
### Environment Customization
After logging in, you may want to configure the environment. Write your
@@ -34,7 +42,7 @@ Do not run commands outputing to standard output (echo, module list,
etc) in .bashrc for non-interactive SSH sessions. It breaks fundamental
functionality (scp, PBS) of your account! Take care for SSH session
interactivity for such commands as id="result_box"
-class="short_text"> class="hps alt-edited">stated
+ class="hps alt-edited">stated
in the previous example.
### Application Modules
@@ -113,3 +121,7 @@ This command expands your searched paths to modules. You can also add
this command to the .bashrc file to expand paths permanently. After this
command, you can use same commands to list/add/remove modules as is
described above.
+
+
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/hardware-overview.md b/converted/docs.it4i.cz/anselm-cluster-documentation/hardware-overview.md
index 39af24ff..e47a9f9f 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/hardware-overview.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/hardware-overview.md
@@ -5,12 +5,20 @@ Hardware Overview
+
+
+
+
+
+
+
+
The Anselm cluster consists of 209 computational nodes named cn[1-209]
of which 180 are regular compute nodes, 23 GPU Kepler K20 accelerated
nodes, 4 MIC Xeon Phi 5110 accelerated nodes and 2 fat nodes. Each node
is a class="WYSIWYG_LINK">powerful x86-64 computer,
equipped with 16 cores (two eight-core Intel Sandy Bridge processors),
-at least 64GB RAM, and local hard drive. The user to the Anselm
+at least 64GB RAM, and local hard drive. The user access to the Anselm
cluster is provided by two login nodes login[1,2]. The nodes are
interlinked by high speed InfiniBand and Ethernet networks. All nodes
share 320TB /home disk storage to store the user files. The 146TB shared
@@ -19,7 +27,7 @@ share 320TB /home disk storage to store the user files. The 146TB shared
The Fat nodes are equipped with large amount (512GB) of memory.
Virtualization infrastructure provides resources to run long term
servers and services in virtual mode. Fat nodes and virtual servers may
- 45 TB of dedicated block storage. Accelerated nodes, fat nodes,
+access 45 TB of dedicated block storage. Accelerated nodes, fat nodes,
and virtualization infrastructure are available [upon
request](https://support.it4i.cz/rt) made by a PI.
@@ -348,9 +356,9 @@ disk storage available on all compute nodes /lscratch. [More about
class="WYSIWYG_LINK">Storage](storage.html).
-The user to the Anselm cluster is provided by two login nodes
-login1, login2, and data mover node dm1. [More about ing
-cluster.](ing-the-cluster.html)
+The user access to the Anselm cluster is provided by two login nodes
+login1, login2, and data mover node dm1. [More about accessing
+cluster.](accessing-the-cluster.html)
The parameters are summarized in the following tables:
@@ -398,3 +406,7 @@ Fat compute node 2x Intel Sandy Bridge E5-2665, 2.4GHz 512GB -
nodes](compute-nodes.html),
[Storage](storage.html), and
[Network](network.html).
+
+
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/introduction.md b/converted/docs.it4i.cz/anselm-cluster-documentation/introduction.md
index 39979bff..8c5f98f7 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/introduction.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/introduction.md
@@ -5,6 +5,14 @@ Introduction
+
+
+
+
+
+
+
+
Welcome to Anselm supercomputer cluster. The Anselm cluster consists of
209 compute nodes, totaling 3344 compute cores with 15TB RAM and giving
over 94 Tflop/s theoretical peak performance. Each node is a
@@ -23,7 +31,7 @@ class="WYSIWYG_LINK">Linux
family.](http://upload.wikimedia.org/wikipedia/commons/1/1b/Linux_Distribution_Timeline.svg)
We have installed a wide range of
[software](software.1.html) packages targeted at
-different scientific domains. These packages are ible via the
+different scientific domains. These packages are accessible via the
[modules environment](environment-and-modules.html).
User data shared file-system (HOME, 320TB) and job data shared
@@ -37,4 +45,8 @@ Read more on how to [apply for
resources](../get-started-with-it4innovations/applying-for-resources.html),
[obtain login
credentials,](../get-started-with-it4innovations/obtaining-login-credentials.html)
-and [ the cluster](accessing-the-cluster.html).
+and [access the cluster](accessing-the-cluster.html).
+
+
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/network.md b/converted/docs.it4i.cz/anselm-cluster-documentation/network.md
index 673a16d7..375b9fd4 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/network.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/network.md
@@ -5,6 +5,14 @@ Network
+
+
+
+
+
+
+
+
All compute and login nodes of Anselm are interconnected by
[Infiniband](http://en.wikipedia.org/wiki/InfiniBand)
QDR network and by Gigabit
@@ -20,7 +28,7 @@ high-bandwidth, low-latency
QDR network (IB 4x QDR, 40 Gbps). The network topology is a fully
non-blocking fat-tree.
-The compute nodes may be ed via the Infiniband network using ib0
+The compute nodes may be accessed via the Infiniband network using ib0
network interface, in address range 10.2.1.1-209. The MPI may be used to
establish native Infiniband connection among the nodes.
@@ -34,7 +42,7 @@ other nodes concurrently.
Ethernet Network
----------------
-The compute nodes may be ed via the regular Gigabit Ethernet
+The compute nodes may be accessed via the regular Gigabit Ethernet
network interface eth0, in address range 10.1.1.1-209, or by using
aliases cn1-cn209.
The network provides **114MB/s** transfer rates via the TCP connection.
@@ -55,5 +63,9 @@ $ ssh 10.2.1.110
$ ssh 10.1.1.108
```
-In this example, we the node cn110 by Infiniband network via the
+In this example, we access the node cn110 by Infiniband network via the
ib0 interface, then from cn110 to cn108 by Ethernet network.
+
+
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/prace.md b/converted/docs.it4i.cz/anselm-cluster-documentation/prace.md
index 22b199c7..ba5c31d0 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/prace.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/prace.md
@@ -5,6 +5,14 @@ PRACE User Support
+
+
+
+
+
+
+
+
Intro
-----
@@ -14,12 +22,12 @@ general documentation applies to them as well. This section shows the
main differences for quicker orientation, but often uses references to
the original documentation. PRACE users who don't undergo the full
procedure (including signing the IT4I AuP on top of the PRACE AuP) will
-not have a password and thus to some services intended for
+not have a password and thus access to some services intended for
regular users. This can lower their comfort, but otherwise they should
be able to use the TIER-1 system as intended. Please see the [Obtaining
Login Credentials
section](../get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials.html),
-if the same level of is required.
+if the same level of access is required.
All general [PRACE User
Documentation](http://www.prace-ri.eu/user-documentation/)
@@ -35,7 +43,7 @@ Helpdesk](http://www.prace-ri.eu/helpdesk-guide264/).
Information about the local services are provided in the [introduction
of general user documentation](introduction.html).
Please keep in mind, that standard PRACE accounts don't have a password
-to the web interface of the local (IT4Innovations) request
+to access the web interface of the local (IT4Innovations) request
tracker and thus a new ticket should be created by sending an e-mail to
support[at]it4i.cz.
@@ -59,7 +67,7 @@ Accessing the cluster
### Access with GSI-SSH
-For all PRACE users the method for interactive (login) and data
+For all PRACE users the method for interactive access (login) and data
transfer based on grid services from Globus Toolkit (GSI SSH and
GridFTP) is supported.
@@ -67,14 +75,14 @@ The user will need a valid certificate and to be present in the PRACE
LDAP (please contact your HOME SITE or the primary investigator of your
project for LDAP account creation).
-Most of the information needed by PRACE users ing the Anselm
+Most of the information needed by PRACE users accessing the Anselm
TIER-1 system can be found here:
- [General user's
FAQ](http://www.prace-ri.eu/Users-General-FAQs)
- [Certificates
FAQ](http://www.prace-ri.eu/Certificates-FAQ)
-- [Interactive using
+- [Interactive access using
GSISSH](http://www.prace-ri.eu/Interactive-Access-Using-gsissh)
- [Data transfer with
GridFTP](http://www.prace-ri.eu/Data-Transfer-with-GridFTP-Details)
@@ -95,9 +103,9 @@ valid 12 hours), use:
-To Anselm cluster, two login nodes running GSI SSH service are
+To access Anselm cluster, two login nodes running GSI SSH service are
available. The service is available from public Internet as well as from
-the internal PRACE network (ible only from other PRACE partners).
+the internal PRACE network (accessible only from other PRACE partners).
Access from PRACE network:**
@@ -162,12 +170,12 @@ gsiscp can be used:
If the user needs to run X11 based graphical application and does not
have a X11 server, the applications can be run using VNC service. If the
-user is using regular SSH based , please see the [section in
+user is using regular SSH based access, please see the [section in
general
documentation](https://docs.it4i.cz/anselm-cluster-documentation/resolveuid/11e53ad0d2fd4c5187537f4baeedff33).
-If the user uses GSI SSH based , then the procedure is similar to
-the SSH based ([look
+If the user uses GSI SSH based access, then the procedure is similar to
+the SSH based access ([look
here](https://docs.it4i.cz/anselm-cluster-documentation/resolveuid/11e53ad0d2fd4c5187537f4baeedff33)),
only the port forwarding must be done using GSI SSH:
@@ -176,7 +184,7 @@ only the port forwarding must be done using GSI SSH:
### Access with SSH
After successful obtainment of login credentials for the local
-IT4Innovations account, the PRACE users can the cluster as
+IT4Innovations account, the PRACE users can access the cluster as
regular users using SSH. For more information please see the [section in
general
documentation](https://docs.it4i.cz/anselm-cluster-documentation/resolveuid/5d3d6f3d873a42e584cbf4365c4e251b).
@@ -192,7 +200,7 @@ documentation](https://docs.it4i.cz/anselm-cluster-documentation/resolveuid/5d3d
Apart from the standard mechanisms, for PRACE users to transfer data
to/from Anselm cluster, a GridFTP server running Globus Toolkit GridFTP
service is available. The service is available from public Internet as
-well as from the internal PRACE network (ible only from other
+well as from the internal PRACE network (accessible only from other
PRACE partners).
There's one control server and three backend servers for striping and/or
@@ -268,8 +276,8 @@ Usage of the cluster
--------------------
There are some limitations for PRACE user when using the cluster. By
-default PRACE users aren't allowed to special queues in the PBS
-Pro to have high priority or exclusive to some special equipment
+default PRACE users aren't allowed to access special queues in the PBS
+Pro to have high priority or exclusive access to some special equipment
like accelerated nodes and high memory (fat) nodes. There may be also
restrictions obtaining a working license for the commercial software
installed on the cluster, mostly because of the license agreement or
@@ -373,3 +381,7 @@ increase.
+
+
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/remote-visualization.md b/converted/docs.it4i.cz/anselm-cluster-documentation/remote-visualization.md
index 8cd08824..41c9e40e 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/remote-visualization.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/remote-visualization.md
@@ -1,12 +1,20 @@
Remote visualization service
============================
+
+
+
+
+
+
+
+
Introduction
------------
The goal of this service is to provide the users a GPU accelerated use
of OpenGL applications, especially for pre- and post- processing work,
-where not only the GPU performance is needed but also fast to the
+where not only the GPU performance is needed but also fast access to the
shared file systems of the cluster and a reasonable amount of RAM.
The service is based on integration of open source tools VirtualGL and
@@ -32,9 +40,9 @@ InfiniBand QDR
Schematic overview
------------------
-
+
-
+
How to use the service
----------------------
@@ -120,7 +128,7 @@ $ ssh login2.anselm.it4i.cz -L 5901:localhost:5901
*If you use Windows and Putty, please refer to port forwarding setup
in the documentation:*
-[https://docs.it4i.cz/anselm-cluster-documentation/ing-the-cluster/x-window-and-vnc#section-12](accessing-the-cluster/x-window-and-vnc.html#section-12)
+[https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/x-window-and-vnc#section-12](accessing-the-cluster/x-window-and-vnc.html#section-12)
#### 7. If you don't have Turbo VNC installed on your workstation. {#7-if-you-don-t-have-turbo-vnc-installed-on-your-workstation}
@@ -138,7 +146,7 @@ $ vncviewer localhost:5901
*If you use Windows version of TurboVNC Viewer, just run the Viewer and
use address **localhost:5901**.*
-#### 9. Proceed to the chapter "Access the visualization node." {#9-proceed-to-the-chapter--the-visualization-node}
+#### 9. Proceed to the chapter "Access the visualization node." {#9-proceed-to-the-chapter-access-the-visualization-node}
*Now you should have working TurboVNC session connected to your
workstation.*
@@ -155,7 +163,7 @@ $ vncserver -kill :1
Access the visualization node
-----------------------------
-To the node use a dedicated PBS Professional scheduler queue
+To access the node use a dedicated PBS Professional scheduler queue
qviz**. The queue has following properties:
<table>
@@ -196,7 +204,7 @@ default/max</th>
</tbody>
</table>
-Currently when ing the node, each user gets 4 cores of a CPU
+Currently when accessing the node, each user gets 4 cores of a CPU
allocated, thus approximately 16 GB of RAM and 1/4 of the GPU capacity.
*If more GPU power or RAM is required, it is recommended to allocate one
whole node per user, so that all 16 cores, whole RAM and whole GPU is
@@ -204,7 +212,7 @@ exclusive. This is currently also the maximum allowed allocation per one
user. One hour of work is allocated by default, the user may ask for 2
hours maximum.*
-To the visualization node, follow these steps:
+To access the visualization node, follow these steps:
#### 1. In your VNC session, open a terminal and allocate a node using PBSPro qsub command. {#1-in-your-vnc-session-open-a-terminal-and-allocate-a-node-using-pbspro-qsub-command}
@@ -281,22 +289,25 @@ Tips and Tricks
If you want to increase the responsibility of the visualization, please
adjust your TurboVNC client settings in this way:
-
+
To have an idea how the settings are affecting the resulting picture
quality three levels of "JPEG image quality" are demonstrated:
1. JPEG image quality = 30
-
+
2. JPEG image quality = 15
-
+
3. JPEG image quality = 10
-
+
+
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/capacity-computing.md b/converted/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/capacity-computing.md
index 5ccce37c..1c23802d 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/capacity-computing.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/capacity-computing.md
@@ -5,6 +5,14 @@ Capacity computing
+
+
+
+
+
+
+
+
Introduction
------------
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/introduction.md b/converted/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/introduction.md
index 4ba64d17..f914ccf6 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/introduction.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/introduction.md
@@ -5,6 +5,14 @@ Resource Allocation and Job Execution
+
+
+
+
+
+
+
+
To run a [job](../introduction.html), [computational
resources](../introduction.html) for this particular job
must be allocated. This is done via the PBS Pro job workload manager
@@ -22,8 +30,8 @@ The resources are allocated to the job in a fairshare fashion, subject
to constraints set by the queue and resources available to the Project.
[The Fairshare](job-priority.html) at Anselm ensures
that individual users may consume approximately equal amount of
-resources per week. The resources are ible via several queues for
-queueing the jobs. The queues provide prioritized and exclusive
+resources per week. The resources are accessible via several queues for
+queueing the jobs. The queues provide prioritized and exclusive access
to the computational resources. Following queues are available to Anselm
users:
@@ -72,3 +80,5 @@ Read more on [Capacity
computing](capacity-computing.html) page.
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-priority.md b/converted/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-priority.md
index e5a5d60e..f51d9e4c 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-priority.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-priority.md
@@ -1,6 +1,14 @@
Job scheduling
==============
+
+
+
+
+
+
+
+
Job execution priority
----------------------
@@ -104,3 +112,5 @@ execution times and better resource usage. Jobs with suitable (small)
walltime could be backfilled - and overtake job(s) with higher priority.
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-submission-and-execution.md b/converted/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-submission-and-execution.md
index 41d61d31..f80fb145 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-submission-and-execution.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-submission-and-execution.md
@@ -5,6 +5,14 @@ Job submission and execution
+
+
+
+
+
+
+
+
Job Submission
--------------
@@ -149,11 +157,19 @@ switch can communicate most efficiently. Sharing the same switch
prevents hops in the network and provides for unbiased, most efficient
network communication.
+
+
+
+
Nodes sharing the same switch may be selected via the PBS resource
attribute ibswitch. Values of this attribute are iswXX, where XX is the
switch number. The node-switch mapping can be seen at [Hardware
Overview](../hardware-overview.html) section.
+
+
+
+
We recommend allocating compute nodes of a single switch when best
possible computational network performance is required to run the job
efficiently:
@@ -176,9 +192,21 @@ Advanced job handling
Intel Turbo Boost Technology is on by default. We strongly recommend
keeping the default.
+
+
+
+
If necessary (such as in case of benchmarking) you can disable the Turbo
for all nodes of the job by using the PBS resource attribute
cpu_turbo_boost
+
+
+
+
+
+
+
+
$ qsub -A OPEN-0-0 -q qprod -l select=4:ncpus=16 -l cpu_turbo_boost=0 -I
More about the Intel Turbo Boost in the TurboBoost section
@@ -369,11 +397,11 @@ $ pwd
In this example, 4 nodes were allocated interactively for 1 hour via the
qexp queue. The interactive shell is executed in the home directory.
-All nodes within the allocation may be ed via ssh. Unallocated
-nodes are not ible to user.
+All nodes within the allocation may be accessed via ssh. Unallocated
+nodes are not accessible to user.
-The allocated nodes are ible via ssh from login nodes. The nodes
-may each other via ssh as well.
+The allocated nodes are accessible via ssh from login nodes. The nodes
+may access each other via ssh as well.
Calculations on allocated nodes may be executed remotely via the MPI,
ssh, pdsh or clush. You may find out which nodes belong to the
@@ -542,3 +570,5 @@ computing](capacity-computing.html) section.
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/resources-allocation-policy.md b/converted/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/resources-allocation-policy.md
index 881fa314..532ef20f 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/resources-allocation-policy.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/resources-allocation-policy.md
@@ -5,6 +5,14 @@ Resources Allocation Policy
+
+
+
+
+
+
+
+
Resources Allocation Policy
---------------------------
@@ -13,8 +21,8 @@ to constraints set by the queue and resources available to the Project.
The Fairshare at Anselm ensures that individual users may consume
approximately equal amount of resources per week. Detailed information
in the [Job scheduling](job-priority.html) section. The
-resources are ible via several queues for queueing the jobs. The
-queues provide prioritized and exclusive to the computational
+resources are accessible via several queues for queueing the jobs. The
+queues provide prioritized and exclusive access to the computational
resources. Following table provides the queue partitioning overview:
@@ -135,7 +143,7 @@ select the proper nodes during the PSB job submission.
- **qprod**, the Production queue****: This queue is intended for
normal production runs. It is required that active project with
nonzero remaining resources is specified to enter the qprod. All
- nodes may be ed via the qprod queue, except the reserved ones.
+ nodes may be accessed via the qprod queue, except the reserved ones.
>*>178 nodes without accelerator are
included.* Full nodes, 16 cores per node
are allocated. The queue runs with medium priority and no special
@@ -144,14 +152,14 @@ select the proper nodes during the PSB job submission.
- **qlong**, the Long queue****: This queue is intended for long
production runs. It is required that active project with nonzero
remaining resources is specified to enter the qlong. Only 60 nodes
- without acceleration may be ed via the qlong queue. Full
+ without acceleration may be accessed via the qlong queue. Full
nodes, 16 cores per node are allocated. The queue runs with medium
priority and no special authorization is required to use it.>
*The maximum runtime in qlong is 144 hours (three times of the
standard qprod time - 3 * 48 h).*
- **qnvidia, qmic, qfat**, the Dedicated queues****: The queue qnvidia
- is dedicated to the Nvidia accelerated nodes, the qmic to
- MIC nodes and qfat the Fat nodes. It is required that active
+ is dedicated to access the Nvidia accelerated nodes, the qmic to
+ access MIC nodes and qfat the Fat nodes. It is required that active
project with nonzero remaining resources is specified to enter
these queues. 23 nvidia, 4 mic and 2 fat nodes are included. Full
nodes, 16 cores per node are allocated. The queues run with>
@@ -168,7 +176,7 @@ select the proper nodes during the PSB job submission.
after exhaustion of computational resources.). It is required that
active project is specified to enter the queue, however no remaining
resources are required. Consumed resources will be accounted to
- the Project. Only 178 nodes without accelerator may be ed from
+ the Project. Only 178 nodes without accelerator may be accessed from
this queue. Full nodes, 16 cores per node are allocated. The queue
runs with very low priority and no special authorization is required
to use it. The maximum runtime in qfree is 12 hours.
@@ -193,7 +201,7 @@ Anselm users may check current queue configuration at
Check the status of jobs, queues and compute nodes at
<https://extranet.it4i.cz/anselm/>
-
+
Display the queue status on Anselm:
@@ -297,3 +305,5 @@ Password:
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys.md
index e1c2bba1..1e398688 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys.md
@@ -1,6 +1,14 @@
Overview of ANSYS Products
==========================
+
+
+
+
+
+
+
+
[SVS FEM](http://www.svsfem.cz/)** as ***[ANSYS
Channel partner](http://www.ansys.com/)*** for Czech
Republic provided all ANSYS licenses for ANSELM cluster and supports of
@@ -14,7 +22,7 @@ are distinguished by "**Academic...**" word in the name of license or
by two letter preposition "**aa_**" in the license feature name. Change
of license is realized on command line respectively directly in user's
pbs file (see individual products). [ id="result_box"
-class="short_text"> More about
+ More about
licensing
here](ansys/licensing.html)
@@ -32,3 +40,5 @@ solution to the Anselm directly from the client's Workbench project
(see ANSYS RSM service).
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-cfx.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-cfx.md
index 6e40eaa7..816d1fa6 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-cfx.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-cfx.md
@@ -1,6 +1,14 @@
ANSYS CFX
=========
+
+
+
+
+
+
+
+
[ANSYS
CFX](http://www.ansys.com/Products/Simulation+Technology/Fluid+Dynamics/Fluid+Dynamics+Products/ANSYS+CFX)
software is a high-performance, general purpose fluid dynamics program
@@ -50,7 +58,7 @@ for host in `cat $PBS_NODEFILE`
do
if [ "$hl" = "" ]
then hl="$host:$procs_per_host"
- else hl="$:$host:$procs_per_host"
+ else hl="${hl}:$host:$procs_per_host"
fi
done
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-fluent.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-fluent.md
index e725ae6a..95062db4 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-fluent.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-fluent.md
@@ -1,6 +1,14 @@
ANSYS Fluent
============
+
+
+
+
+
+
+
+
[ANSYS
Fluent](http://www.ansys.com/Products/Simulation+Technology/Fluid+Dynamics/Fluid+Dynamics+Products/ANSYS+Fluent)
software contains the broad physical modeling capabilities needed to
@@ -148,6 +156,14 @@ execute the job across multiple processors.
+
+
+
+
+
+
+
+
>To run ANSYS Fluent in batch mode with user's config file you can
utilize/modify the following script and execute it via the qsub
command.
@@ -180,7 +196,7 @@ command.
cpus=‘expr $num_nodes * $NCPUS‘
#Default arguments for mpp jobs, these should be changed to suit your
#needs.
- fluent_args="-t$ $fluent_args -cnf=$PBS_NODEFILE"
+ fluent_args="-t${cpus} $fluent_args -cnf=$PBS_NODEFILE"
;;
*)
#SMP case
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-ls-dyna.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-ls-dyna.md
index 0369b68d..e8b84ab2 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-ls-dyna.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-ls-dyna.md
@@ -1,9 +1,17 @@
ANSYS LS-DYNA
=============
+
+
+
+
+
+
+
+
[ANSYS
LS-DYNA](http://www.ansys.com/Products/Simulation+Technology/Structural+Mechanics/Explicit+Dynamics/ANSYS+LS-DYNA)
-software provides convenient and easy-to-use to the
+software provides convenient and easy-to-use access to the
technology-rich, time-tested explicit solver without the need to contend
with the complex input requirements of this sophisticated program.
Introduced in 1996, ANSYS LS-DYNA capabilities have helped customers in
@@ -59,7 +67,7 @@ for host in `cat $PBS_NODEFILE`
do
if [ "$hl" = "" ]
then hl="$host:$procs_per_host"
- else hl="$:$host:$procs_per_host"
+ else hl="${hl}:$host:$procs_per_host"
fi
done
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-mechanical-apdl.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-mechanical-apdl.md
index 37287cff..84f086b2 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-mechanical-apdl.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-mechanical-apdl.md
@@ -1,6 +1,14 @@
ANSYS MAPDL
===========
+
+
+
+
+
+
+
+
>**[ANSYS
Multiphysics](http://www.ansys.com/Products/Simulation+Technology/Structural+Mechanics/ANSYS+Multiphysics)**
software offers a comprehensive product solution for both multiphysics
@@ -45,7 +53,7 @@ for host in `cat $PBS_NODEFILE`
do
if [ "$hl" = "" ]
then hl="$host:$procs_per_host"
- else hl="$:$host:$procs_per_host"
+ else hl="${hl}:$host:$procs_per_host"
fi
done
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ls-dyna.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ls-dyna.md
index 3591982a..66362a0d 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ls-dyna.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ls-dyna.md
@@ -1,6 +1,14 @@
LS-DYNA
=======
+
+
+
+
+
+
+
+
[LS-DYNA](http://www.lstc.com/) is a multi-purpose,
explicit and implicit finite element program used to analyze the
nonlinear dynamic response of structures. Its fully automated contact
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/chemistry/molpro.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/chemistry/molpro.md
index ade13a15..b526aaea 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/chemistry/molpro.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/chemistry/molpro.md
@@ -1,8 +1,20 @@
Molpro
======
+
+
+
+
Molpro is a complete system of ab initio programs for molecular
electronic structure calculations.
+
+
+
+
+
+
+
+
About Molpro
------------
@@ -14,7 +26,7 @@ License
-------
Molpro software package is available only to users that have a valid
-license. Please contact support to enable to Molpro if you have a
+license. Please contact support to enable access to Molpro if you have a
valid license appropriate for running on our cluster (eg. >academic
research group licence, parallel execution).
@@ -89,3 +101,5 @@ these are placed in the fast scratch filesystem.
rm -rf /scratch/$USER/$PBS_JOBID
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/chemistry/nwchem.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/chemistry/nwchem.md
index 9ee1499e..c32bc8e5 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/chemistry/nwchem.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/chemistry/nwchem.md
@@ -1,7 +1,19 @@
NWChem
======
+
+
+
+
High-Performance Computational Chemistry
+
+
+
+
+
+
+
+
>Introduction
-------------------------
@@ -64,3 +76,5 @@ in the input file set the following directives :
"direct" mode, eg. "scf direct"
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/compilers.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/compilers.md
index dc8f123e..c088e8fb 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/compilers.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/compilers.md
@@ -1,11 +1,23 @@
Compilers
=========
+
+
+
+
Available compilers, including GNU, INTEL and UPC compilers
+
+
+
+
+
+
+
+
Currently there are several compilers for different programming
languages available on the Anselm cluster:
@@ -32,7 +44,7 @@ GNU C/C++ and Fortran Compilers
For compatibility reasons there are still available the original (old
4.4.6-4) versions of GNU compilers as part of the OS. These are
-ible in the search path by default.
+accessible in the search path by default.
It is strongly recommended to use the up to date version (4.8.1) which
comes with the module gcc:
@@ -163,3 +175,5 @@ For information how to work with nVidia CUDA, please read the [nVidia
CUDA page](nvidia-cuda.html).
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/comsol/comsol-multiphysics.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/comsol/comsol-multiphysics.md
index 8019d803..0490ce30 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/comsol/comsol-multiphysics.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/comsol/comsol-multiphysics.md
@@ -5,11 +5,19 @@ COMSOL Multiphysics®
+
+
+
+
+
+
+
+
>>Introduction
-------------------------
->>[COMSOL](http://www.comsol.com)><span>
+>>[COMSOL](http://www.comsol.com)
is a powerful environment for modelling and solving various engineering
and scientific problems based on partial differential equations. COMSOL
is designed to solve coupled or multiphysics phenomena. For many
@@ -37,7 +45,7 @@ applications.
others](http://www.comsol.com/products)
>>COMSOL also allows an
->>><span>interface support for
+>>interface support for
equation-based modelling of
>>partial differential
equations.
@@ -49,18 +57,18 @@ equations.
>>On the Anselm cluster COMSOL is available in the latest
stable version. There are two variants of the release:
-- >>**Non commercial**><span> or so
+- >>**Non commercial** or so
called >>**EDU
variant**>>, which can be used for research
and educational purposes.
-- >>**Commercial**><span> or so called
- >>**COM variant**><span>,
+- >>**Commercial** or so called
+ >>**COM variant**,
which can used also for commercial activities.
- >>**COM variant**><span>
+ >>**COM variant**
has only subset of features compared to the
>>**EDU
- variant**>> available.
+ variant**>> available. <span
id="result_box"
More about
licensing will be posted here
@@ -73,7 +81,7 @@ stable version. There are two variants of the release:
$ module load comsol
```
->>By default the ><span>**EDU
+>>By default the **EDU
variant**>> will be loaded. If user needs other
version or variant, load the particular version. To obtain the list of
available versions use
@@ -121,7 +129,7 @@ module load comsol
ntask=$(wc -l $PBS_NODEFILE)
-comsol -nn $ batch -configuration /tmp –mpiarg –rmk –mpiarg pbs -tmpdir /scratch/$USER/ -inputfile name_input_f.mph -outputfile name_output_f.mph -batchlog name_log_f.log
+comsol -nn ${ntask} batch -configuration /tmp –mpiarg –rmk –mpiarg pbs -tmpdir /scratch/$USER/ -inputfile name_input_f.mph -outputfile name_output_f.mph -batchlog name_log_f.log
```
>>Working directory has to be created before sending the
@@ -130,25 +138,25 @@ has to be in working directory or full path to input file has to be
specified. The appropriate path to the temp directory of the job has to
be set by command option (-tmpdir).
-LiveLink™* *for MATLAB^®^
+LiveLink™* *for MATLAB®^
-------------------------
>>COMSOL is the software package for the numerical solution of
the partial differential equations. LiveLink for MATLAB allows
connection to the
-COMSOL>>^><span><span><span><span>**®**</span></span></span></span></span>^
+COMSOL>><span><span><span><span><span>**®**</span></span></span></span></span>^
API (Application Programming Interface) with the benefits of the
programming language and computing environment of the MATLAB.
>>LiveLink for MATLAB is available in both
->>**EDU**><span> and
->>**COM**><span>
->>**variant**><span> of the
+>>**EDU** and
+>>**COM**
+>>**variant** of the
COMSOL release. On Anselm 1 commercial
-(>>**COM**><span>) license
+(>>**COM**) license
and the 5 educational
-(>>**EDU**><span>) licenses
+(>>**EDU**) licenses
of LiveLink for MATLAB (please see the [ISV
Licenses](../isv_licenses.html)) are available.
Following example shows how to start COMSOL model from MATLAB via
@@ -192,7 +200,7 @@ module load comsol/43b-EDU
ntask=$(wc -l $PBS_NODEFILE)
-comsol -nn $ server -configuration /tmp -mpiarg -rmk -mpiarg pbs -tmpdir /scratch/$USER &
+comsol -nn ${ntask} server -configuration /tmp -mpiarg -rmk -mpiarg pbs -tmpdir /scratch/$USER &
cd /apps/engineering/comsol/comsol43b/mli
matlab -nodesktop -nosplash -r "mphstart; addpath /scratch/$USER; test_job"
```
@@ -205,3 +213,7 @@ path to input file has to be specified. The Matlab command option (-r
”mphstart”) created a connection with a COMSOL server using the default
port number.
+
+
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers.md
index 50587938..719aee66 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers.md
@@ -5,6 +5,14 @@ Debuggers and profilers summary
+
+
+
+
+
+
+
+
Introduction
------------
@@ -90,3 +98,5 @@ Read more at
the [Vampir](../../salomon/software/debuggers/vampir.html) page.
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-ddt.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-ddt.md
index 6397524f..10f99442 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-ddt.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-ddt.md
@@ -5,6 +5,14 @@ Allinea Forge (DDT,MAP)
+
+
+
+
+
+
+
+
Allinea Forge consist of two tools - debugger DDT and profiler MAP.
Allinea DDT, is a commercial debugger primarily for debugging parallel
@@ -61,11 +69,11 @@ $ mpif90 -g -O0 -o test_debug test.f
Before debugging, you need to compile your code with theses flags:
--g** : Generates extra debugging information usable by GDB. -g3
+-g** : Generates extra debugging information usable by GDB. -g3**
includes even more debugging information. This option is available for
GNU and INTEL C/C++ and Fortran compilers.
--O0** : Suppress all optimizations.
+-O0** : Suppress all optimizations.**
@@ -77,7 +85,7 @@ forwarding enabled. This could mean using the -X in the ssh:
$ ssh -X username@anselm.it4i.cz
-Other options is to login node using VNC. Please see the detailed
+Other options is to access login node using VNC. Please see the detailed
information on how to [use graphic user interface on
Anselm](https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/resolveuid/11e53ad0d2fd4c5187537f4baeedff33)
.
@@ -130,3 +138,5 @@ Debugging with Allinea DDT, Workshop conducted at LLNL by Allinea on May
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-performance-reports.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-performance-reports.md
index 16c14756..77f9ce55 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-performance-reports.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-performance-reports.md
@@ -1,11 +1,23 @@
Allinea Performance Reports
===========================
+
+
+
+
quick application profiling
+
+
+
+
+
+
+
+
Introduction
------------
@@ -75,3 +87,7 @@ and
[mympiprog_32p*.html](mympiprog_32p_2014-10-15_16-56.html)
were created. We can see that the code is very efficient on MPI and is
CPU bounded.
+
+
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/cube.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/cube.md
index d84e0da1..80a5cdfd 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/cube.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/cube.md
@@ -1,6 +1,14 @@
CUBE
====
+
+
+
+
+
+
+
+
Introduction
------------
@@ -22,6 +30,10 @@ dimension is organized by files and routines in your source code etc.
+
+
+
+
@@ -70,3 +82,5 @@ performance data will be available.
1.<http://www.scalasca.org/software/cube-4.x/download.html>
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/intel-performance-counter-monitor.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/intel-performance-counter-monitor.md
index 7ad500b8..90174f56 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/intel-performance-counter-monitor.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/intel-performance-counter-monitor.md
@@ -1,6 +1,14 @@
Intel Performance Counter Monitor
=================================
+
+
+
+
+
+
+
+
Introduction
------------
@@ -85,7 +93,7 @@ Usage: > pcm-power.x <delay> |
### pcm
This command provides an overview of performance counters and memory
-usage. >Usage: > pcm.x
+usage. >Usage: > <span pcm.x
<delay> | <external program>
Sample output :
@@ -207,7 +215,7 @@ installed on Anselm.
API
---
-In a similar fashion to PAPI, PCM provides a C++ API to the
+In a similar fashion to PAPI, PCM provides a C++ API to access the
performance counter from within your application. Refer to the [doxygen
documentation](http://intel-pcm-api-documentation.github.io/classPCM.html)
for details of the API.
@@ -300,3 +308,5 @@ References
Documentation
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/intel-vtune-amplifier.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/intel-vtune-amplifier.md
index b4569b28..eeffc7a7 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/intel-vtune-amplifier.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/intel-vtune-amplifier.md
@@ -5,6 +5,14 @@ Intel VTune Amplifier
+
+
+
+
+
+
+
+
Introduction
------------
@@ -19,7 +27,11 @@ highlight of the features:
bandwidth
- Power usage analysis - frequency and sleep states.
-
+
+
+
+
+
@@ -110,3 +122,7 @@ References
1.><https://www.rcac.purdue.edu/tutorials/phi/PerformanceTuningXeonPhi-Tullos.pdf> Performance
Tuning for Intel® Xeon Phi™ Coprocessors
+
+
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/papi.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/papi.md
index 580197ae..59406fda 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/papi.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/papi.md
@@ -5,11 +5,19 @@ PAPI
+
+
+
+
+
+
+
+
Introduction
------------
dir="auto">Performance Application Programming
-Interface >(PAPI) is a portable interface to
+Interface >(PAPI) is a portable interface to access
hardware performance counters (such as instruction counts and cache
misses) found in most modern architectures. With the new component
framework, PAPI is not limited only to CPU counters, but offers also
@@ -102,6 +110,10 @@ PAPI provides two kinds of events:
- **Native events **is a set of all events supported by the
current hardware. This is a larger set of features than preset. For
other components than CPU, only native events are usually available.
+
+
+
+
To use PAPI in your application, you need to link the appropriate
include file.
@@ -110,6 +122,10 @@ include file.
- f90papi.h for Fortran 90
- fpapi.h for Fortran with preprocessor
+
+
+
+
The include path is automatically added by papi module to
$INCLUDE.
@@ -269,3 +285,5 @@ References
3.<http://icl.cs.utk.edu/papi/docs/> API Documentation
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/scalasca.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/scalasca.md
index 3fff2cf0..697152de 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/scalasca.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/scalasca.md
@@ -1,6 +1,14 @@
Scalasca
========
+
+
+
+
+
+
+
+
>Introduction
-------------------------
@@ -107,3 +115,5 @@ References
1.<http://www.scalasca.org/>
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/score-p.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/score-p.md
index 15482da4..1a8e7cd8 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/score-p.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/score-p.md
@@ -1,6 +1,14 @@
Score-P
=======
+
+
+
+
+
+
+
+
Introduction
------------
@@ -21,7 +29,7 @@ on Anselm :
- class="s1">scorep/1.2.3-gcc-openmpi>, for usage
with [GNU
- Compiler](../compilers.html)> and [OpenMPI](../mpi-1/Running_OpenMPI.html)>,</span>
+ Compiler](../compilers.html)> and [OpenMPI](../mpi-1/Running_OpenMPI.html){.internal>,</span>
- class="s1">scorep/1.2.3-icc-impi>, for usage
with [Intel
@@ -146,3 +154,6 @@ Again, please refer to the
[documentation](https://silc.zih.tu-dresden.de/scorep-current/pdf/scorep.pdf)
for a more elaborate description.
+
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/summary.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/summary.md
index b60cde8f..b8bced0e 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/summary.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/summary.md
@@ -5,6 +5,14 @@ Debuggers and profilers summary
+
+
+
+
+
+
+
+
Introduction
------------
@@ -85,3 +93,7 @@ Vampir is a GUI trace analyzer for traces in OTF format.
Read more at
the [Vampir](../../../salomon/software/debuggers/vampir.html) page.
+
+
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/total-view.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/total-view.md
index e7bb3eb1..80c232cd 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/total-view.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/total-view.md
@@ -1,8 +1,20 @@
Total View
==========
+
+
+
+
TotalView is a GUI-based source code multi-process, multi-thread
debugger.
+
+
+
+
+
+
+
+
License and Limitations for Anselm Users
----------------------------------------
@@ -51,11 +63,11 @@ Compile the code:
Before debugging, you need to compile your code with theses flags:
--g** : Generates extra debugging information usable by GDB. -g3
+-g** : Generates extra debugging information usable by GDB. -g3**
includes even more debugging information. This option is available for
GNU and INTEL C/C++ and Fortran compilers.
--O0** : Suppress all optimizations.
+-O0** : Suppress all optimizations.**
Starting a Job with TotalView
-----------------------------
@@ -65,7 +77,7 @@ using the -X in the ssh:
ssh -X username@anselm.it4i.cz
-Other options is to login node using VNC. Please see the detailed
+Other options is to access login node using VNC. Please see the detailed
information on how to use graphic user interface on Anselm
[here](https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/resolveuid/11e53ad0d2fd4c5187537f4baeedff33#VNC).
@@ -92,8 +104,8 @@ Please note:** To be able to run parallel debugging procedure from the
command line without stopping the debugger in the mpiexec source code
you have to add the following function to your **~/.tvdrc** file:
- proc mpi_auto_run_starter {
- set starter_programs
+ proc mpi_auto_run_starter {loaded_id} {
+ set starter_programs {mpirun mpiexec orterun}
set executable_name [TV::symbol get $loaded_id full_pathname]
set file_component [file tail $executable_name]
@@ -161,3 +173,7 @@ Documentation
documentation](http://www.roguewave.com/support/product-documentation/totalview-family.aspx#totalview)
web page is a good resource for learning more about some of the advanced
TotalView features.
+
+
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/valgrind.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/valgrind.md
index 77fcfe6a..2123bb93 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/valgrind.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/valgrind.md
@@ -1,7 +1,19 @@
Valgrind
========
+
+
+
+
Valgrind is a tool for memory debugging and profiling.
+
+
+
+
+
+
+
+
About Valgrind
--------------
@@ -20,8 +32,8 @@ Valgrind run 5-100 times slower.
The main tools available in Valgrind are :
- **Memcheck**, the original, must used and default tool. Verifies
- memory in you program and can detect use of unitialized
- memory, out of bounds memory , memory leaks, double free, etc.
+ memory access in you program and can detect use of unitialized
+ memory, out of bounds memory access, memory leaks, double free, etc.
- **Massif**, a heap profiler.
- **Hellgrind** and **DRD** can detect race conditions in
multi-threaded applications.
@@ -116,7 +128,7 @@ description of command line options.
==12652== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 6 from 6)
In the output we can see that Valgrind has detected both errors - the
-off-by-one memory at line 5 and a memory leak of 40 bytes. If we
+off-by-one memory access at line 5 and a memory leak of 40 bytes. If we
want a detailed analysis of the memory leak, we need to run Valgrind
with --leak-check=full option :
@@ -288,3 +300,7 @@ launched MPI process)
We can see that Valgrind has reported use of unitialised memory on the
master process (which reads the array to be broadcasted) and use of
unaddresable memory on both processes.
+
+
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/vampir.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/vampir.md
index f073038c..c61edbc8 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/vampir.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/vampir.md
@@ -1,6 +1,14 @@
Vampir
======
+
+
+
+
+
+
+
+
Vampir is a commercial trace analysis and visualisation tool. It can
work with traces in OTF and OTF2 formats. It does not have the
functionality to collect traces, you need to use a trace collection tool
@@ -32,3 +40,5 @@ References
1.<https://www.vampir.eu>
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/gpi2.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/gpi2.md
index 954fbca2..c4d0de9c 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/gpi2.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/gpi2.md
@@ -1,11 +1,23 @@
GPI-2
=====
+
+
+
+
A library that implements the GASPI specification
+
+
+
+
+
+
+
+
Introduction
------------
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite.md
index 048a009a..16b07fef 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite.md
@@ -5,6 +5,14 @@ Intel Parallel Studio
+
+
+
+
+
+
+
+
The Anselm cluster provides following elements of the Intel Parallel
Studio XE
@@ -94,3 +102,5 @@ Read more at the [Intel TBB](intel-suite/intel-tbb.html)
page.
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-compilers.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-compilers.md
index 92023bac..790c7160 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-compilers.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-compilers.md
@@ -5,6 +5,14 @@ Intel Compilers
+
+
+
+
+
+
+
+
The Intel compilers version 13.1.1 are available, via module intel. The
compilers include the icc C and C++ compiler and the ifort fortran
77/90/95 compiler.
@@ -67,3 +75,5 @@ doing >this:
will result in larger binaries.
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-debugger.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-debugger.md
index 1b6fc1c2..5199e190 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-debugger.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-debugger.md
@@ -5,6 +5,14 @@ Intel Debugger
+
+
+
+
+
+
+
+
Debugging serial applications
-----------------------------
@@ -23,7 +31,7 @@ The debugger may run in text mode. To debug in text mode, use
$ idbc
To debug on the compute nodes, module intel must be loaded.
-The GUI on compute nodes may be ed using the same way as in [the
+The GUI on compute nodes may be accessed using the same way as in [the
GUI
section](https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/resolveuid/11e53ad0d2fd4c5187537f4baeedff33)
@@ -40,7 +48,7 @@ Example:
In this example, we allocate 1 full compute node, compile program
myprog.c with debugging options -O0 -g and run the idb debugger
-interactively on the myprog.x executable. The GUI is via X11 port
+interactively on the myprog.x executable. The GUI access is via X11 port
forwarding provided by the PBS workload manager.
Debugging parallel applications
@@ -98,3 +106,5 @@ website,
<http://software.intel.com/sites/products/documentation/doclib/stdxe/2013/composerxe/debugger/user_guide/index.htm>
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-integrated-performance-primitives.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-integrated-performance-primitives.md
index 0945105c..14d9e68d 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-integrated-performance-primitives.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-integrated-performance-primitives.md
@@ -5,6 +5,14 @@ Intel IPP
+
+
+
+
+
+
+
+
Intel Integrated Performance Primitives
---------------------------------------
@@ -95,3 +103,5 @@ in particular the [IPP Reference
manual.](http://software.intel.com/sites/products/documentation/doclib/ipp_sa/71/ipp_manual/index.htm)
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-mkl.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-mkl.md
index 2a84fe48..dfc8761d 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-mkl.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-mkl.md
@@ -6,6 +6,14 @@ Intel MKL
+
+
+
+
+
+
+
+
Intel Math Kernel Library
-------------------------
@@ -87,7 +95,7 @@ With intel compiler use -mkl option to link default threaded MKL.
The MKL library provides number of interfaces. The fundamental once are
the LP64 and ILP64. The Intel MKL ILP64 libraries use the 64-bit integer
-type (necessary for indexing large arrays, with more than 2^31^-1
+type (necessary for indexing large arrays, with more than 231^-1
elements), whereas the LP64 libraries index arrays with the 32-bit
integer type.
@@ -195,3 +203,5 @@ particular the [MKL users
guide](https://software.intel.com/en-us/intel-mkl/documentation/linux).
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-parallel-studio-introduction.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-parallel-studio-introduction.md
index d4a7b981..50600509 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-parallel-studio-introduction.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-parallel-studio-introduction.md
@@ -5,6 +5,14 @@ Intel Parallel Studio
+
+
+
+
+
+
+
+
The Anselm cluster provides following elements of the Intel Parallel
Studio XE
@@ -91,3 +99,5 @@ manner.
Read more at the [Intel TBB](intel-tbb.html) page.
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-tbb.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-tbb.md
index c9dde88e..7a4cae0c 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-tbb.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-tbb.md
@@ -5,6 +5,14 @@ Intel TBB
+
+
+
+
+
+
+
+
Intel Threading Building Blocks
-------------------------------
@@ -55,3 +63,5 @@ Read more on Intel website,
<http://software.intel.com/sites/products/documentation/doclib/tbb_sa/help/index.htm>
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi.md
index 21ac1ca8..1a3933de 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi.md
@@ -1,11 +1,23 @@
Intel Xeon Phi
==============
+
+
+
+
A guide to Intel Xeon Phi usage
+
+
+
+
+
+
+
+
Intel Xeon Phi can be programmed in several modes. The default mode on
Anselm is offload mode, but all modes described in this document are
supported.
@@ -13,7 +25,7 @@ supported.
Intel Utilities for Xeon Phi
----------------------------
-To get to a compute node with Intel Xeon Phi accelerator, use the
+To get access to a compute node with Intel Xeon Phi accelerator, use the
PBS interactive session
$ qsub -I -q qmic -A NONE-0-0
@@ -404,7 +416,7 @@ Phi:
### Execution of the Program in Native Mode on Intel Xeon Phi
-The user to the Intel Xeon Phi is through the SSH. Since user
+The user access to the Intel Xeon Phi is through the SSH. Since user
home directories are mounted using NFS on the accelerator, users do not
have to copy binary files or libraries between the host and accelerator.
@@ -662,7 +674,7 @@ Similarly to execution of OpenMP programs in native mode, since the
environmental module are not supported on MIC, user has to setup paths
to Intel MPI libraries and binaries manually. One time setup can be done
by creating a "**.profile**" file in user's home directory. This file
-sets up the environment on the MIC automatically once user to the
+sets up the environment on the MIC automatically once user access to the
accelerator through the SSH.
$ vim ~/.profile
@@ -684,7 +696,7 @@ libraries.
library and particular version of an Intel compiler. These versions have
to match with loaded modules.
-To a MIC accelerator located on a node that user is currently
+To access a MIC accelerator located on a node that user is currently
connected to, use:
$ ssh mic0
@@ -756,7 +768,7 @@ execute:
Execution on host - MPI processes distributed over multiple
accelerators on multiple nodes**
->To get to multiple nodes with MIC accelerator, user has to
+>To get access to multiple nodes with MIC accelerator, user has to
use PBS to allocate the resources. To start interactive session, that
allocates 2 compute nodes = 2 MIC accelerators run qsub command with
following parameters:
@@ -777,7 +789,7 @@ immediately. To see the other nodes that have been allocated use:
cn205.bullx
>This output means that the PBS allocated nodes cn204 and cn205,
-which means that user has direct to "**cn204-mic0**" and
+which means that user has direct access to "**cn204-mic0**" and
"**cn-205-mic0**" accelerators.
>Please note: At this point user can connect to any of the
@@ -937,11 +949,11 @@ PBS also generates a set of node-files that can be used instead of
manually creating a new one every time. Three node-files are genereated:
Host only node-file:**
- - /lscratch/$/nodefile-cn
+ - /lscratch/${PBS_JOBID}/nodefile-cn
MIC only node-file**:
- - /lscratch/$/nodefile-mic
+ - /lscratch/${PBS_JOBID}/nodefile-mic
Host and MIC node-file**:
- - /lscratch/$/nodefile-mix
+ - /lscratch/${PBS_JOBID}/nodefile-mix
Please note each host or accelerator is listed only per files. User has
to specify how many jobs should be executed per node using "-n"
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses.md
index 667b7c11..75b279db 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses.md
@@ -1,11 +1,23 @@
ISV Licenses
============
+
+
+
+
A guide to managing Independent Software Vendor licences
+
+
+
+
+
+
+
+
On Anselm cluster there are also installed commercial software
applications, also known as ISV (Independent Software Vendor), which are
subjects to licensing. The licenses are limited and their usage may be
@@ -24,7 +36,7 @@ non-commercial version.
Overview of the licenses usage
------------------------------
-The overview is generated every minute and is ible from web or
+The overview is generated every minute and is accessible from web or
command line interface.
### Web interface
@@ -40,7 +52,7 @@ number of free license features
For each license there is a unique text file, which provides the
information about the name, number of available (purchased/licensed),
number of used and number of free license features. The text files are
-ible from the Anselm command prompt.
+accessible from the Anselm command prompt.
Product File with license state Note
------------ ----------------------------------------------------- ---------------------
@@ -80,7 +92,7 @@ Each feature of each license is accounted and checked by the scheduler
of PBS Pro. If you ask for certain licences, the scheduler won't start
the job until the asked licenses are free (available). This prevents to
crash batch jobs, just because of id="result_box"
-class="short_text"> unavailability of the
+ unavailability of the
needed licenses.
The general format of the name is:
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/java.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/java.md
index 6bf87d7f..294e7901 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/java.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/java.md
@@ -1,11 +1,23 @@
Java
====
+
+
+
+
Java on ANSELM
+
+
+
+
+
+
+
+
Java is available on Anselm cluster. Activate java by loading the java
module
@@ -33,3 +45,5 @@ you require the java interface to MPI, please contact [Anselm
support](https://support.it4i.cz/rt/).
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/kvirtualization.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/kvirtualization.md
index 38885466..9acb9278 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/kvirtualization.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/kvirtualization.md
@@ -1,11 +1,23 @@
Virtualization
==============
+
+
+
+
Running virtual machines on compute nodes
+
+
+
+
+
+
+
+
Introduction
------------
@@ -18,7 +30,7 @@ needs.
tools
- Application requires specific setup (installation, configuration) of
complex software stack
-- Application requires privileged to operating system
+- Application requires privileged access to operating system
- ... and combinations of above cases
We offer solution for these cases - **virtualization**. Anselm's
@@ -85,7 +97,7 @@ running in their virtual machines.
We propose this job workflow:
-
+Workflow](virtualization-job-workflow "Virtualization Job Workflow")
Our recommended solution is that job script creates distinct shared job
directory, which makes a central point for data exchange between
@@ -223,7 +235,7 @@ for 5 minutes, then shutdown virtual machine.
### Create job script for executing virtual machine
Create job script according recommended id="result_box"
-class="short_text">
+
[Virtual Machine Job
Workflow](virtualization.html#virtual-machine-job-workflow).
@@ -231,7 +243,7 @@ Example job for Windows virtual machine:
#/bin/sh
- JOB_DIR=/scratch/$USER/win/$
+ JOB_DIR=/scratch/$USER/win/${PBS_JOBID}
#Virtual machine settings
VM_IMAGE=~/work/img/win.img
@@ -239,25 +251,25 @@ Example job for Windows virtual machine:
VM_SMP=16
# Prepare job dir
- mkdir -p $ && cd $ || exit 1
+ mkdir -p ${JOB_DIR} && cd ${JOB_DIR} || exit 1
ln -s ~/work/win .
ln -s /scratch/$USER/data .
ln -s ~/work/win/script/run/run-appl.bat run.bat
# Run virtual machine
- export TMPDIR=/lscratch/$
+ export TMPDIR=/lscratch/${PBS_JOBID}
module add qemu
qemu-system-x86_64
-enable-kvm
-cpu host
- -smp $
- -m $
+ -smp ${VM_SMP}
+ -m ${VM_MEMORY}
-vga std
-localtime
-usb -usbdevice tablet
-device virtio-net-pci,netdev=net0
- -netdev user,id=net0,smb=$,hostfwd=tcp::3389-:3389
- -drive file=$,media=disk,if=virtio
+ -netdev user,id=net0,smb=${JOB_DIR},hostfwd=tcp::3389-:3389
+ -drive file=${VM_IMAGE},media=disk,if=virtio
-snapshot
-nographic
@@ -299,9 +311,9 @@ Run virtual machine (simple)
$ qemu-system-x86_64 -hda win.img -enable-kvm -cpu host -smp 16 -m 32768 -vga std -localtime -usb -usbdevice tablet -vnc :0
-You can virtual machine by VNC viewer (option -vnc) connecting to
+You can access virtual machine by VNC viewer (option -vnc) connecting to
IP address of compute node. For VNC you must use [VPN
-network](../../ing-the-cluster/vpn-access.html).
+network](../../accessing-the-cluster/vpn-access.html).
Install virtual machine from iso file
@@ -316,10 +328,10 @@ sharing and port forwarding, in snapshot mode
$ qemu-system-x86_64 -drive file=win.img,media=disk,if=virtio -enable-kvm -cpu host -smp 16 -m 32768 -vga std -localtime -usb -usbdevice tablet -device virtio-net-pci,netdev=net0 -netdev user,id=net0,smb=/scratch/$USER/tmp,hostfwd=tcp::3389-:3389 -vnc :0 -snapshot
-Thanks to port forwarding you can virtual machine via SSH (Linux)
+Thanks to port forwarding you can access virtual machine via SSH (Linux)
or RDP (Windows) connecting to IP address of compute node (and port 2222
for SSH). You must use [VPN
-network](../../ing-the-cluster/vpn-access.html).
+network](../../accessing-the-cluster/vpn-access.html).
Keep in mind, that if you use virtio devices, you must have virtio
drivers installed on your virtual machine.
@@ -334,7 +346,7 @@ SMB sharing, port forwarding.
In default configuration IP network 10.0.2.0/24 is used, host has IP
address 10.0.2.2, DNS server 10.0.2.3, SMB server 10.0.2.4 and virtual
machines obtain address from range 10.0.2.15-10.0.2.31. Virtual machines
-have to Anselm's network via NAT on compute node (host).
+have access to Anselm's network via NAT on compute node (host).
Simple network setup
@@ -353,9 +365,9 @@ Optimized network setup with sharing and port forwarding
### Advanced networking
-Internet **
+Internet access**
-Sometime your virtual machine needs to internet (install
+Sometime your virtual machine needs access to internet (install
software, updates, software activation, etc). We suggest solution using
Virtual Distributed Ethernet (VDE) enabled QEMU with SLIRP running on
login node tunnelled to compute node. Be aware, this setup has very low
@@ -479,7 +491,7 @@ file (and discarded after virtual machine exits). **It is strongly
recommended mode for running your jobs.** Set TMPDIR environment
variable to local scratch directory for placement temporary files.
- $ export TMPDIR=/lscratch/$
+ $ export TMPDIR=/lscratch/${PBS_JOBID}
$ qemu-system-x86_64 ... -snapshot
### Windows guests
@@ -489,3 +501,5 @@ For Windows guests we recommend these options, life will be easier:
$ qemu-system-x86_64 ... -localtime -usb -usbdevice tablet
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/Running_OpenMPI.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/Running_OpenMPI.md
index c8ae4858..94f4063b 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/Running_OpenMPI.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/Running_OpenMPI.md
@@ -5,6 +5,14 @@ Running OpenMPI
+
+
+
+
+
+
+
+
OpenMPI program execution
-------------------------
@@ -273,3 +281,5 @@ Some options have changed in OpenMPI version 1.8.
</table>
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/mpi.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/mpi.md
index c74b65cb..52cd3f2d 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/mpi.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/mpi.md
@@ -5,6 +5,14 @@ MPI
+
+
+
+
+
+
+
+
Setting up MPI Environment
--------------------------
@@ -150,7 +158,7 @@ scratch /lscratch filesystem.
### Ways to run MPI programs
Optimal way to run an MPI program depends on its memory requirements,
-memory pattern and communication pattern.
+memory access pattern and communication pattern.
Consider these ways to run an MPI program:
1. One MPI process per node, 16 threads per process
@@ -161,13 +169,13 @@ One MPI** process per node, using 16 threads, is most useful for
memory demanding applications, that make good use of processor cache
memory and are not memory bound. This is also a preferred way for
communication intensive applications as one process per node enjoys full
-bandwidth to the network interface.
+bandwidth access to the network interface.
Two MPI** processes per node, using 8 threads each, bound to processor
socket is most useful for memory bandwidth bound applications such as
BLAS1 or FFT, with scalable memory demand. However, note that the two
-processes will share to the network interface. The 8 threads and
-socket binding should ensure maximum memory bandwidth and
+processes will share access to the network interface. The 8 threads and
+socket binding should ensure maximum memory access bandwidth and
minimize communication, migration and numa effect overheads.
Important! Bind every OpenMP thread to a core!
@@ -199,3 +207,5 @@ more on [how to run Intel MPI on
accelerators](../intel-xeon-phi.html).
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/mpi4py-mpi-for-python.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/mpi4py-mpi-for-python.md
index 725ccf16..2eee46e1 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/mpi4py-mpi-for-python.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/mpi4py-mpi-for-python.md
@@ -1,11 +1,23 @@
MPI4Py (MPI for Python)
=======================
+
+
+
+
OpenMPI interface to Python
+
+
+
+
+
+
+
+
Introduction
------------
@@ -105,3 +117,5 @@ More examples and documentation can be found on [MPI for Python
webpage](https://pythonhosted.org/mpi4py/usrman/index.html).
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/running-mpich2.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/running-mpich2.md
index e228281a..c8cd47ec 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/running-mpich2.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/running-mpich2.md
@@ -5,12 +5,20 @@ Running MPICH2
+
+
+
+
+
+
+
+
MPICH2 program execution
------------------------
The MPICH2 programs use mpd daemon or ssh connection to spawn processes,
no PBS support is needed. However the PBS allocation is required to
- compute nodes. On Anselm, the **Intel MPI** and **mpich2 1.9**
+access compute nodes. On Anselm, the **Intel MPI** and **mpich2 1.9**
are MPICH2 based MPI implementations.
### Basic usage
@@ -193,3 +201,5 @@ chapter](../intel-xeon-phi.html) provides details on how
to run Intel MPI code on Xeon Phi architecture.
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/copy_of_matlab.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/copy_of_matlab.md
index 05905cd8..79a4d0e6 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/copy_of_matlab.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/copy_of_matlab.md
@@ -5,6 +5,14 @@ Matlab
+
+
+
+
+
+
+
+
Introduction
------------
@@ -36,12 +44,12 @@ Matlab on the compute nodes via PBS Pro scheduler.
If you require the Matlab GUI, please follow the general informations
about [running graphical
-applications](../../../get-started-with-it4innovations/ing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html).
+applications](../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html).
Matlab GUI is quite slow using the X forwarding built in the PBS (qsub
-X), so using X11 display redirection either via SSH or directly by
xauth (please see the "GUI Applications on Compute Nodes over VNC" part
-[here](../../../get-started-with-it4innovations/ing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html))
+[here](../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html))
is recommended.
To run Matlab with GUI, use
@@ -97,7 +105,7 @@ Anselm.
Following example shows how to start interactive session with support
for Matlab GUI. For more information about GUI based applications on
Anselm see [this
-page](../../../get-started-with-it4innovations/ing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html).
+page](../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html).
$ xhost +
$ qsub -I -v DISPLAY=$(uname -n):$(echo $DISPLAY | cut -d ':' -f 2) -A NONE-0-0 -q qexp -l select=1 -l walltime=00:30:00
@@ -109,7 +117,7 @@ The second part of the command shows how to request all necessary
licenses. In this case 1 Matlab-EDU license and 48 Distributed Computing
Engines licenses.
-Once the to compute nodes is granted by PBS, user can load
+Once the access to compute nodes is granted by PBS, user can load
following modules and start Matlab:
r1i0n17$ module load MATLAB/2015b-EDU
@@ -349,3 +357,5 @@ mode](copy_of_matlab.html#parallel-matlab-batch-job-in-local-mode),
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/introduction.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/introduction.md
index 320a5663..31eb1129 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/introduction.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/introduction.md
@@ -1,11 +1,23 @@
Numerical languages
===================
+
+
+
+
Interpreted languages for numerical computations and analysis
+
+
+
+
+
+
+
+
Introduction
------------
@@ -15,7 +27,7 @@ primarily intended for numerical computations.
Matlab
------
-MATLAB^®^ is a high-level language and interactive environment for
+MATLAB®^ is a high-level language and interactive environment for
numerical computation, visualization, and programming.
$ module load MATLAB/2015b-EDU
@@ -48,3 +60,5 @@ computing and graphics.
Read more at the [R page](r.html).
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/matlab.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/matlab.md
index ed43615d..386ed44e 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/matlab.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/matlab.md
@@ -5,6 +5,14 @@ Matlab 2013-2014
+
+
+
+
+
+
+
+
Introduction
------------
@@ -71,7 +79,7 @@ non-interactive PBS sessions. This mode guarantees that the data
processing is not performed on login nodes, but all processing is on
compute nodes.
-
+ 
For the performance reasons Matlab should use system MPI. On Anselm the
supported MPI implementation for Matlab is Intel MPI. To switch to
@@ -92,7 +100,7 @@ be exactly the same as in the following listing:
mpl = strcat(mpich, 'libmpl.so');
opa = strcat(mpich, 'libopa.so');
- extras = ;
+ extras = {};
System MPI library allows Matlab to communicate through 40Gbps
Infiniband QDR interconnect instead of slower 1Gb ethernet network.
@@ -124,7 +132,7 @@ The second part of the command shows how to request all necessary
licenses. In this case 1 Matlab-EDU license and 32 Distributed Computing
Engines licenses.
-Once the to compute nodes is granted by PBS, user can load
+Once the access to compute nodes is granted by PBS, user can load
following modules and start Matlab:
cn79$ module load matlab/R2013a-EDU
@@ -264,3 +272,5 @@ compute nodes number of workers start-up time[s]
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/octave.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/octave.md
index 04e38a45..f4843c40 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/octave.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/octave.md
@@ -5,6 +5,14 @@ Octave
+
+
+
+
+
+
+
+
Introduction
------------
@@ -150,3 +158,5 @@ other mechanism) will actually run slower than on host CPU.
>
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/r.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/r.md
index c507ac4f..a9edbe52 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/r.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/r.md
@@ -5,6 +5,14 @@ R
+
+
+
+
+
+
+
+
Introduction
------------
@@ -34,12 +42,12 @@ Modules
-------
**The R version 3.0.1 is available on Anselm, along with GUI interface
-Rstudio**
+Rstudio
Application Version module
------------- -------------- ---------
R** R 3.0.1 R
-Rstudio**** Rstudio 0.97 Rstudio
+Rstudio** Rstudio 0.97 Rstudio
$ module load R
@@ -55,10 +63,10 @@ OMP_NUM_THREADS environment variable.
### Interactive execution
-To run R interactively, using Rstudio** GUI, log in with ssh -X parameter
+To run R interactively, using Rstudio GUI, log in with ssh -X parameter
for X11 forwarding. Run rstudio:
- $ module load Rstudio**
+ $ module load Rstudio
$ rstudio
### Batch execution
@@ -391,7 +399,7 @@ The above is the mpi.apply MPI example for calculating the number π.
Only the slave processes carry out the calculation. Note the
mpi.parSapply(), ** function call. The package
parallel
-[example](r.html#package-parallel)[above](r.html#package-parallel)
+[example](r.html#package-parallel)[above](r.html#package-parallel){.anchor
may be trivially adapted (for much better performance) to this structure
using the mclapply() in place of mpi.parSapply().
@@ -446,3 +454,8 @@ and general [MPI](../mpi-1.html) sections.
+
+
+
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/fftw.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/fftw.md
index c35d9412..a5a568ee 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/fftw.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/fftw.md
@@ -1,11 +1,23 @@
FFTW
====
+
+
+
+
The discrete Fourier transform in one or more dimensions, MPI parallel
+
+
+
+
+
+
+
+
FFTW is a C subroutine library for computing the discrete Fourier
@@ -153,3 +165,7 @@ program](../mpi-1/running-mpich2.html).
Read more on FFTW usage on the [FFTW
website.](http://www.fftw.org/fftw3_doc/)
+
+
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/gsl.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/gsl.md
index 00ea8e87..1e7ef10d 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/gsl.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/gsl.md
@@ -1,12 +1,24 @@
GSL
===
+
+
+
+
The GNU Scientific Library. Provides a wide range of mathematical
routines.
+
+
+
+
+
+
+
+
Introduction
------------
@@ -164,3 +176,6 @@ library search path is compiled in, so that no modules are necessary to
run the code.
+
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/hdf5.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/hdf5.md
index 13b8f367..5048c00c 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/hdf5.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/hdf5.md
@@ -1,7 +1,19 @@
HDF5
====
+
+
+
+
Hierarchical Data Format library. Serial and MPI parallel version.
+
+
+
+
+
+
+
+
[HDF5 (Hierarchical Data Format)](http://www.hdfgroup.org/HDF5/) is a
@@ -154,10 +166,10 @@ Example
status = H5Dread(dataset_id, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT,
dset_data);
- /* End to the dataset and release resources used by it. */
+ /* End access to the dataset and release resources used by it. */
status = H5Dclose(dataset_id);
- /* Terminate to the data space. */
+ /* Terminate access to the data space. */
status = H5Sclose(dataspace_id);
/* Close the file. */
@@ -184,9 +196,13 @@ For further informations, please see the website:
-class="smarterwiki-popup-bubble smarterwiki-popup-bubble-active smarterwiki-popup-bubble-flipped">
+
class="smarterwiki-popup-bubble-tip">
-class="smarterwiki-popup-bubble-body">
-class="smarterwiki-popup-bubble-links-container">
-class="smarterwiki-popup-bubble-links">
-btnI=I'm+Feeling+Lucky&btnI=I'm+Feeling+Lucky&q=HDF5%20icc%20serial%09pthread%09hdf5%2F1.8.13%09%24HDF5_INC%20%24HDF5_SHLIB%09%24HDF5_INC%20%24HDF5_CPP_LIB%09%24HDF5_INC%20%24HDF5_F90_LIB%0A%0AHDF5%20icc%20parallel%20MPI%0A%09pthread%2C%20IntelMPI%09hdf5-parallel%2F1.8.13%09%24HDF5_INC%20%24HDF5_SHLIB%09Not%20supported%09%24HDF5_INC%20%24HDF5_F90_LIB+wikipedia "Search Wikipedia"){.smarterwiki-popup-bubble-link}</span>
+
+
+
+btnI=I'm+Feeling+Lucky&btnI=I'm+Feeling+Lucky&q=HDF5%20icc%20serial%09pthread%09hdf5%2F1.8.13%09%24HDF5_INC%20%24HDF5_SHLIB%09%24HDF5_INC%20%24HDF5_CPP_LIB%09%24HDF5_INC%20%24HDF5_F90_LIB%0A%0AHDF5%20icc%20parallel%20MPI%0A%09pthread%2C%20IntelMPI%09hdf5-parallel%2F1.8.13%09%24HDF5_INC%20%24HDF5_SHLIB%09Not%20supported%09%24HDF5_INC%20%24HDF5_F90_LIB+wikipedia "Search Wikipedia"){.smarterwiki-popup-bubble</span>
+
+
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/intel-numerical-libraries.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/intel-numerical-libraries.md
index 2304f2fd..3d307a11 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/intel-numerical-libraries.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/intel-numerical-libraries.md
@@ -1,11 +1,23 @@
Intel numerical libraries
=========================
+
+
+
+
Intel libraries for high performance in numerical computing
+
+
+
+
+
+
+
+
Intel Math Kernel Library
-------------------------
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/magma-for-intel-xeon-phi.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/magma-for-intel-xeon-phi.md
index 7fa0a444..f0113b1a 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/magma-for-intel-xeon-phi.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/magma-for-intel-xeon-phi.md
@@ -1,8 +1,20 @@
MAGMA for Intel Xeon Phi
========================
+
+
+
+
Next generation dense algebra library for heterogeneous systems with
accelerators
+
+
+
+
+
+
+
+
### Compiling and linking with MAGMA
To be able to compile and link code with MAGMA library user has to load
@@ -90,3 +102,7 @@ Jack Dongarra et. al,
[http://icl.utk.edu/projectsfiles/magma/pubs/24-MAGMA_MIC_03.pdf
](http://icl.utk.edu/projectsfiles/magma/pubs/24-MAGMA_MIC_03.pdf)
+
+
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/petsc.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/petsc.md
index ebb0f189..42272de8 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/petsc.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/petsc.md
@@ -1,6 +1,10 @@
PETSc
=====
+
+
+
+
PETSc is a suite of building blocks for the scalable solution of
scientific and engineering applications modelled by partial differential
equations. It supports MPI, shared memory, and GPUs through CUDA or
@@ -9,6 +13,14 @@ OpenCL, as well as hybrid MPI-shared memory or MPI-GPU parallelism.
+
+
+
+
+
+
+
+
Introduction
------------
@@ -47,7 +59,7 @@ names obey this pattern:
module load petsc/3.4.4-icc-impi-mkl-opt
where `variant` is replaced by one of
-``. The `opt` variant is compiled
+`{dbg, opt, threads-dbg, threads-opt}`. The `opt` variant is compiled
without debugging information (no `-g` option) and with aggressive
compiler optimizations (`-O3 -xAVX`). This variant is suitable for
performance measurements and production runs. In all other cases use the
@@ -104,3 +116,7 @@ petsc module loaded.
- [Trilinos ML](http://trilinos.sandia.gov/packages/ml/)
- [SPAI - Sparse Approximate
Inverse](https://bitbucket.org/petsc/pkg-spai)
+
+
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/trilinos.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/trilinos.md
index 81b90738..63d71568 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/trilinos.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/trilinos.md
@@ -1,8 +1,20 @@
Trilinos
========
+
+
+
+
Packages for large scale scientific and engineering problems. Provides
MPI and hybrid parallelization.
+
+
+
+
+
+
+
+
### Introduction
Trilinos is a collection of software packages for the numerical solution
@@ -66,7 +78,7 @@ or
include Makefile.export.<package>
if you are interested only in a specific Trilinos package. This will
-give you to the variables such as Trilinos_CXX_COMPILER,
+give you access to the variables such as Trilinos_CXX_COMPILER,
Trilinos_INCLUDE_DIRS, Trilinos_LIBRARY_DIRS etc. For the detailed
description and example makefile see
<http://trilinos.sandia.gov/Export_Makefile.txt>.
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda.md
index 38f69e38..952c9285 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda.md
@@ -1,11 +1,23 @@
nVidia CUDA
===========
+
+
+
+
A guide to nVidia CUDA programming and GPU usage
+
+
+
+
+
+
+
+
CUDA Programming on Anselm
--------------------------
@@ -41,7 +53,7 @@ the example used is deviceQuery) and run "make" to start the compilation
$ cd ~/cuda-samples/1_Utilities/deviceQuery
$ make
-To run the code user can use PBS interactive session to get to a
+To run the code user can use PBS interactive session to get access to a
node from qnvidia queue (note: use your project name with parameter -A
in the qsub command) and execute the binary file
@@ -185,7 +197,7 @@ This code can be compiled using following command
$ nvcc test.cu -o test_cuda
-To run the code use interactive PBS session to get to one of the
+To run the code use interactive PBS session to get access to one of the
GPU accelerated nodes
$ qsub -I -q qnvidia -A OPEN-0-0
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/diagnostic-component-team.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/diagnostic-component-team.md
index 994fc86a..c6c822b5 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/diagnostic-component-team.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/diagnostic-component-team.md
@@ -6,15 +6,23 @@ Diagnostic component (TEAM)
+
+
+
+
+
+
+
+
### Access
TEAM is available at the following address
: <http://omics.it4i.cz/team/>
-The address is ible only via
-[VPN. ](../../ing-the-cluster/vpn-access.html)
+The address is accessible only via
+[VPN. ](../../accessing-the-cluster/vpn-access.html)
-### Diagnostic component (TEAM)
+### Diagnostic component (TEAM) {#diagnostic-component-team}
VCF files are scanned by this diagnostic tool for known diagnostic
disease-associated variants. When no diagnostic mutation is found, the
@@ -33,11 +41,11 @@ diagnostic is produced. TEAM also provides with an interface for the
definition of and customization of panels, by means of which, genes and
mutations can be added or discarded to adjust panel definitions.
-
-
-
-
-
+
@@ -46,10 +54,15 @@ mutations can be added or discarded to adjust panel definitions.
*Figure 5. ****Interface of the application. Panels for defining
targeted regions of interest can be set up by just drag and drop known
disease genes or disease definitions from the lists. Thus, virtual
-panels can be
+panels can be interactively improved as the knowledge of the disease
increases.*
*
*
+
+
+
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/overview.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/overview.md
index a7b30eed..01bfba86 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/overview.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/overview.md
@@ -1,11 +1,23 @@
Overview
========
+
+
+
+
The human NGS data processing solution
+
+
+
+
+
+
+
+
Introduction
------------
@@ -20,15 +32,15 @@ mapping and variant calling steps that result in a file containing the
set of variants in the sample. From this point, the prioritization
component or the diagnostic component can be launched.
-
-
-
-
-
-
-
-
-
+
*Figure 1.*** *OMICS MASTER solution overview. Data is produced in the
external labs and comes to IT4I (represented by the blue dashed line).
@@ -37,7 +49,7 @@ annotations for each sequenced patient. These lists files together with
primary and secondary (alignment) data files are stored in IT4I sequence
DB and uploaded to the discovery (candidate prioritization) or
diagnostic component where they can be analyzed directly by the user
-that produced
+that produced them, depending of the experimental design carried
out*. style="text-align: left; ">
Typical genomics pipelines are composed by several components that need
@@ -85,22 +97,22 @@ These steps are carried out over the original FASTQ file with optimized
scripts and includes the following steps: sequence cleansing, estimation
of base quality scores, elimination of duplicates and statistics.
-Input:** FASTQ file.
+Input: FASTQ file.
-Output:** FASTQ file plus an HTML file containing statistics on the
+Output: FASTQ file plus an HTML file containing statistics on the
data.
FASTQ format
>It represents the nucleotide sequence and its corresponding
quality scores.
-
-*Figure 2.****** FASTQ file.***
+
+*Figure 2.**FASTQ file.**
#### Mapping
-Component:** Hpg-aligner.****
+Component:** Hpg-aligner.**
Sequence reads are mapped over the human reference genome. SOLiD reads
are not covered by this solution; they should be mapped with specific
@@ -113,7 +125,7 @@ most common scenarios). This proposal provides a simple and fast
solution that maps almost all the reads, even those containing a high
number of mismatches or indels.
-Input:** FASTQ file.
+Input: FASTQ file.
Output:** Aligned file in BAM format.****
@@ -124,7 +136,7 @@ its alignment is represented on a single line. The format can represent
unmapped reads, reads that are mapped to unique locations, and reads
that are mapped to multiple locations.
->The SAM format ^(1)^> consists of one header
+>The SAM format (1)^> consists of one header
section and one alignment section. The lines in the header section start
with character ‘@’, and lines in the alignment section do not. All lines
are TAB delimited.
@@ -181,7 +193,7 @@ corresponding information is unavailable.
<tr class="even">
<td align="left"><p>7</p></td>
<td align="left"><p>MRNM </p></td>
-<td align="left"><p>Mate REference NaMe ('=^' if same RNAME)</p></td>
+<td align="left"><p>Mate REference NaMe ('=' if same RNAME)</p></td>
</tr>
<tr class="odd">
<td align="left"><p>8</p></td>
@@ -220,21 +232,21 @@ soft clipping, ‘H’ for hard clipping and ‘P’ for padding. These support
splicing, clipping, multi-part and padded alignments. Figure 3 shows
examples of CIGAR strings for different types of alignments.
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
*
Figure 3.*** *SAM format file. The ‘@SQ’ line in the header section
gives the order of reference sequences. Notably, r001 is the name of a
@@ -279,7 +291,7 @@ Component:** GATK.
Identification of single nucleotide variants and indels on the
alignments is performed using the Genome Analysis Toolkit (GATK). GATK
-^(2)^ is a software package developed at the Broad Institute to analyze
+(2)^ is a software package developed at the Broad Institute to analyze
high-throughput sequencing data. The toolkit offers a wide variety of
tools, with a primary focus on variant discovery and genotyping as well
as strong emphasis on data quality assurance.
@@ -290,7 +302,7 @@ Output:** VCF
Variant Call Format (VCF)**
->VCF ^(3)^> is a standardized format for storing the
+>VCF (3)^> is a standardized format for storing the
most prevalent types of sequence variation, including SNPs, indels and
larger structural variants, together with rich annotations. The format
was developed with the primary intention to represent human genetic
@@ -328,26 +340,26 @@ delimited and the number of fields in each data line must match the
number of fields in the header line. It is strongly recommended that all
annotation tags used are declared in the VCF header section.
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
Figure 4.**> (a) Example of valid VCF. The header lines
##fileformat and #CHROM are mandatory, the rest is optional but
@@ -363,11 +375,11 @@ SAMPLE1) and a replacement of two bases by another base (SAMPLE2); the
second line shows a SNP and an insertion; the third a SNP; the fourth a
large structural variant described by the annotation in the INFO column,
the coordinate is that of the base before the variant. (b–f ) Alignments
-and VCF
-
-
-
-
+and VCF representations of different sequence variants: SNP, insertion,
+deletion, replacement, and a large deletion. The REF columns shows the
+reference bases replaced by the haplotype in the ALT column. The
+coordinate refers to the first reference base. (g) Users are advised to
+use simplest representation possible and lowest coordinate in cases
where the position is ambiguous.
### >Annotating
@@ -379,7 +391,7 @@ using the HPG-Variant software, which extracts from CellBase**,** the
Knowledge database, all the information relevant on the predicted
pathologic effect of the variants.
-VARIANT (VARIant Analysis Tool) ^(4)^ reports information on the
+VARIANT (VARIant Analysis Tool) (4)^ reports information on the
variants found that include consequence type and annotations taken from
different databases and repositories (SNPs and variants from dbSNP and
1000 genomes, and disease-related variants from the Genome-Wide
@@ -393,58 +405,58 @@ conventional reports beyond the coding regions and expands the knowledge
on the contribution of non-coding or synonymous variants to the
phenotype studied.
-Input:** VCF
+Input:** VCF**
Output:** The output of this step is the Variant Calling Format (VCF)
file, which contains changes with respect to the reference genome with
-the corresponding QC and functional annotations.
+the corresponding QC and functional annotations.**
#### CellBase
-CellBase^(5)^ is a relational database integrates biological information
+CellBase(5)^ is a relational database integrates biological information
from different sources and includes:
-Core features:**
+**Core features:**
We took genome sequences, genes, transcripts, exons, cytobands or cross
references (xrefs) identifiers (IDs) >from Ensembl
-^(6)^>. Protein information including sequences, xrefs or
+(6)^>. Protein information including sequences, xrefs or
protein features (natural variants, mutagenesis sites,
post-translational modifications, etc.) were imported from UniProt
-^(7)^>.
+(7)^>.
-Regulatory:**
+**Regulatory:**
-CellBase imports miRNA from miRBase ^(8)^; curated and non-curated miRNA
-targets from miRecords ^(9)^, >miRTarBase ^(10)^>,
-TargetScan^(11)^> and microRNA.org ^(12)^> and
+CellBase imports miRNA from miRBase (8)^; curated and non-curated miRNA
+targets from miRecords (9)^, >miRTarBase ^(10)^>,
+TargetScan(11)^> and microRNA.org ^(12)^> and
CpG islands and conserved regions from the UCSC database
-^(13)^>.> </span>
+(13)^>.> </span>
-Functional annotation**
+**Functional annotation**
-OBO Foundry ^(14)^ develops many biomedical ontologies that are
+OBO Foundry (14)^ develops many biomedical ontologies that are
implemented in OBO format. We designed a SQL schema to store these OBO
ontologies and >30 ontologies were imported. OBO ontology term
-annotations were taken from Ensembl ^(6)^. InterPro ^(15)^ annotations
+annotations were taken from Ensembl (6)^. InterPro ^(15)^ annotations
were also imported.
-Variation**
+**Variation**
-CellBase includes SNPs from dbSNP ^(16)^; SNP population frequencies
-from HapMap ^(17)^, 1000 genomes project ^(18)^ and Ensembl ^(6)^;
+CellBase includes SNPs from dbSNP (16)^; SNP population frequencies
+from HapMap (17)^, 1000 genomes project ^(18)^ and Ensembl ^(6)^;
phenotypically annotated SNPs were imported from NHRI GWAS Catalog
-^(19)^,^ ^>HGMD ^(20)^>, Open Access GWAS Database
-^(21)^>, UniProt ^(7)^> and OMIM
-^(22)^>; mutations from COSMIC ^(23)^> and
+(19)^,^ ^>HGMD ^(20)^>, Open Access GWAS Database
+(21)^>, UniProt ^(7)^> and OMIM
+(22)^>; mutations from COSMIC ^(23)^> and
structural variations from Ensembl
-^(6)^>.> </span>
+(6)^>.> </span>
-Systems biology**
+**Systems biology**
We also import systems biology information like interactome information
-from IntAct ^(24)^. Reactome ^(25)^> stores pathway and interaction
-information in BioPAX ^(26)^> format. BioPAX data exchange
+from IntAct (24)^. Reactome ^(25)^> stores pathway and interaction
+information in BioPAX (26)^> format. BioPAX data exchange
format >enables the integration of diverse pathway
resources. We successfully solved the problem of storing data released
in BioPAX format into a SQL relational schema, which allowed us
@@ -610,34 +622,38 @@ should use the next command:
speed-up mapping high-quality reads,
and *Smith-Waterman*> (SW) to increase sensitivity when
reads cannot be mapped using BWT.
-- >>>[hpg-fastq](http://docs.bioinfo.cipf.es/projects/fastqhpc/wiki), <span> a
+- >[hpg-fastq](http://docs.bioinfo.cipf.es/projects/fastqhpc/wiki), > a
quality control tool for high throughput
sequence data.
-- >>><span>[hpg-variant](http://wiki.opencb.org/projects/hpg/doku.php?id=variant:downloads), <span>The
+- >>[hpg-variant](http://wiki.opencb.org/projects/hpg/doku.php?id=variant:downloads), <span>The
HPG Variant suite is an ambitious project aimed to provide a
complete suite of tools to work with genomic variation data, from
VCF tools to variant profiling or genomic statistics. It is being
implemented using High Performance Computing technologies to provide
the best performance possible.</span>
-- >>><span>[picard](http://picard.sourceforge.net/), <span>Picard
+- >>[picard](http://picard.sourceforge.net/), <span>Picard
comprises Java-based command-line utilities that manipulate SAM
files, and a Java API (HTSJDK) for creating new programs that read
and write SAM files. Both SAM text format and SAM binary (BAM)
format are supported.</span>
-- >>><span>[samtools](http://samtools.sourceforge.net/samtools-c.shtml), <span>SAM
+- >>[samtools](http://samtools.sourceforge.net/samtools-c.shtml), <span>SAM
Tools provide various utilities for manipulating alignments in the
SAM format, including sorting, merging, indexing and generating
alignments in a
per-position format.</span>
-- >>>[snpEff](http://snpeff.sourceforge.net/), <span>Genetic
+- >><span>[snpEff](http://snpeff.sourceforge.net/), <span>Genetic
variant annotation and effect
prediction toolbox.</span></span>
+
+
+
+
This listing show which tools are used in each step of the pipeline :
-<!-- -->
+
- >stage-00: fastqc
- >stage-01: hpg_fastq
@@ -692,9 +708,9 @@ button the diagnostic process starts.*
Once the file has been uploaded, a panel must be chosen from the Panel
list. Then, pressing the Run button the diagnostic process starts. TEAM
searches first for known diagnostic mutation(s) taken from four
-databases: HGMD-public ^(20)^,
+databases: HGMD-public (20)^,
[HUMSAVAR](http://www.uniprot.org/docs/humsavar),
-ClinVar ^(29)^ and COSMIC ^(23)^.
+ClinVar (29)^ and COSMIC ^(23)^.
+The address is accessible only
+via [VPN. ](../../accessing-the-cluster/vpn-access.html)
### >BiERApp
@@ -31,11 +39,11 @@ the context of a large-scale genomic project carried out by the Spanish
Network for Research, in Rare Diseases (CIBERER) and the Medical Genome
Project. in which more than 800 exomes have been analyzed.
-
-
-
-
-
+
*Figure 6***. *Web interface to the prioritization tool.* *This
figure* *shows the interface of the web tool for candidate gene
@@ -45,3 +53,4 @@ the variants in the corresponding genomic coordinates.*
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/openfoam.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/openfoam.md
index cc9609e7..81b56414 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/openfoam.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/openfoam.md
@@ -1,11 +1,23 @@
OpenFOAM
========
+
+
+
+
A free, open source CFD software package
+
+
+
+
+
+
+
+
Introduction**
----------------
@@ -29,21 +41,21 @@ For example syntax of available OpenFOAM module is:
>< openfoam/2.2.1-icc-openmpi1.6.5-DP >
this means openfoam version >2.2.1 compiled by
->ICC compiler with >openmpi1.6.5 in> double
+>ICC compiler with >openmpi1.6.5 in<span> double
precision.
Naming convection of the installed versions is following:
>
-openfoam/<>VERSION>>-<</span>>COMPILER</span><span>>-<</span><span>openmpiVERSION</span><span>>-<</span><span>PRECISION</span><span>></span>
+openfoam/<>VERSION>>-<</span><span>COMPILER</span><span>>-<</span><span>openmpiVERSION</span><span>>-<</span><span>PRECISION</span><span>></span>
-- ><>VERSION>> - version of
+- ><>VERSION<span>> - version of
openfoam
- ><>COMPILER> - version of used
compiler
- ><>openmpiVERSION> - version of used
openmpi/impi
-- ><>PRECISION> - DP/>SP –
+- ><>PRECISION> - DP/<span>SP –
double/single precision
###Available OpenFOAM modules**
@@ -118,6 +130,10 @@ Running Serial Applications**
>Create a Bash script >test.sh
+
+
+
+
>
>
@@ -160,8 +176,16 @@ here](../resource-allocation-and-job-execution/job-submission-and-execution.html
>Run the second case for example external incompressible turbulent
flow - case - motorBike.
+
+
+
+
>First we must run serial application bockMesh and decomposePar for
preparation of parallel computation.
+
+
+
+
>
@@ -206,7 +230,7 @@ preparation of parallel computation.
>>This job create simple block mesh and domain decomposition.
Check your decomposition, and submit parallel computation:
->>Create a PBS script>
+>>Create a PBS script<span>
testParallel.pbs:</span>
@@ -225,11 +249,11 @@ testParallel.pbs:</span>
nproc = 32
- mpirun -hostfile $ -np $nproc snappyHexMesh -overwrite -parallel | tee snappyHexMesh.log
+ mpirun -hostfile ${PBS_NODEFILE} -np $nproc snappyHexMesh -overwrite -parallel | tee snappyHexMesh.log
- mpirun -hostfile $ -np $nproc potentialFoam -noFunctionObject-writep -parallel | tee potentialFoam.log
+ mpirun -hostfile ${PBS_NODEFILE} -np $nproc potentialFoam -noFunctionObject-writep -parallel | tee potentialFoam.log
- mpirun -hostfile $ -np $nproc simpleFoam -parallel | tee simpleFoam.log
+ mpirun -hostfile ${PBS_NODEFILE} -np $nproc simpleFoam -parallel | tee simpleFoam.log
>
@@ -260,6 +284,10 @@ testParallel.pbs:</span>
$ cd $FOAM_RUN/
>Create directory applications/solvers in user directory
+
+
+
+
>
$ mkdir -p applications/solvers
$ cd applications/solvers
@@ -276,6 +304,10 @@ testParallel.pbs:</span>
$ cd My_icoFoam
+
+
+
+
>Rename icoFoam.C to My_icoFOAM.C
@@ -293,6 +325,10 @@ testParallel.pbs:</span>
icoFoam.C
EXE = $(FOAM_APPBIN)/icoFoam
+
+
+
+
>and change to:
@@ -318,8 +354,12 @@ testParallel.pbs:</span>
Have a fun with OpenFOAM :)**
- id="__caret"> id="__caret">
+ id="__caret">
+
+
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/operating-system.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/operating-system.md
index 34467f1d..d20265f4 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/operating-system.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/operating-system.md
@@ -1,11 +1,23 @@
Operating System
================
+
+
+
+
The operating system, deployed on ANSELM
+
+
+
+
+
+
+
+
The operating system on Anselm is Linux - bullx Linux Server release
6.3.
@@ -13,3 +25,5 @@ bullx Linux is based on Red Hat Enterprise Linux. bullx Linux is a Linux
distribution provided by Bull and dedicated to HPC applications.
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/paraview.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/paraview.md
index 32970cd1..e0888d8f 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/paraview.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/paraview.md
@@ -1,12 +1,24 @@
ParaView
========
+
+
+
+
An open-source, multi-platform data analysis and visualization
application
+
+
+
+
+
+
+
+
Introduction
------------
@@ -121,3 +133,5 @@ will not take advantage of accelerated nodes on Anselm. Support for GPU
acceleration might be added in the future.
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/storage-1/cesnet-data-storage.md b/converted/docs.it4i.cz/anselm-cluster-documentation/storage-1/cesnet-data-storage.md
index be82b6fa..1f006bd5 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/storage-1/cesnet-data-storage.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/storage-1/cesnet-data-storage.md
@@ -5,6 +5,14 @@ CESNET Data Storage
+
+
+
+
+
+
+
+
Introduction
------------
@@ -23,7 +31,7 @@ Republic.
User of data storage CESNET (DU) association can become organizations or
an individual person who is either in the current employment
relationship (employees) or the current study relationship (students) to
-a legal entity (organization) that meets the “Principles for to
+a legal entity (organization) that meets the “Principles for access to
CESNET Large infrastructure (Access Policy)”.
User may only use data storage CESNET for data transfer and storage
@@ -37,12 +45,12 @@ The service is documented at
please contact directly CESNET Storage Department via e-mail
[du-support(at)cesnet.cz](mailto:du-support@cesnet.cz).
-The procedure to obtain the CESNET is quick and trouble-free.
+The procedure to obtain the CESNET access is quick and trouble-free.
(source
[https://du.cesnet.cz/](https://du.cesnet.cz/wiki/doku.php/en/start "CESNET Data Storage"))
-CESNET storage
+CESNET storage access
---------------------
### Understanding Cesnet storage
@@ -51,7 +59,7 @@ It is very important to understand the Cesnet storage before uploading
data. Please read
<https://du.cesnet.cz/en/navody/home-migrace-plzen/start> first.
-Once registered for CESNET Storage, you may [ the
+Once registered for CESNET Storage, you may [access the
storage](https://du.cesnet.cz/en/navody/faq/start) in
number of ways. We recommend the SSHFS and RSYNC methods.
@@ -59,7 +67,7 @@ number of ways. We recommend the SSHFS and RSYNC methods.
SSHFS: The storage will be mounted like a local hard drive
-The SSHFS provides a very convenient way to the CESNET Storage.
+The SSHFS provides a very convenient way to access the CESNET Storage.
The storage will be mounted onto a local directory, exposing the vast
CESNET Storage as if it was a local removable harddrive. Files can be
than copied in and out in a usual fashion.
@@ -74,7 +82,7 @@ Mount tier1_home **(only 5120M !)**:
$ sshfs username@ssh.du1.cesnet.cz:. cesnet/
-For easy future from Anselm, install your public key
+For easy future access from Anselm, install your public key
$ cp .ssh/id_rsa.pub cesnet/.ssh/authorized_keys
@@ -92,7 +100,7 @@ Once done, please remember to unmount the storage
$ fusermount -u cesnet
-### Rsync
+### Rsync access
Rsync provides delta transfer for best performance, can resume
interrupted transfers
@@ -127,3 +135,7 @@ in the Storage VO
$ rsync --progress -av username@ssh.du1.cesnet.cz:VO_storage-cache_tape/datafolder .
Transfer rates of about 28MB/s can be expected.
+
+
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/storage-1/storage.md b/converted/docs.it4i.cz/anselm-cluster-documentation/storage-1/storage.md
index 5fa2b975..8bf8b095 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/storage-1/storage.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/storage-1/storage.md
@@ -5,10 +5,18 @@ Storage
+
+
+
+
+
+
+
+
There are two main shared file systems on Anselm cluster, the
[HOME](../storage.html#home) and
[SCRATCH](../storage.html#scratch). All login and compute
-nodes may same data on shared filesystems. Compute nodes are also
+nodes may access same data on shared filesystems. Compute nodes are also
equipped with local (non-shared) scratch, ramdisk and tmp filesystems.
Archiving
@@ -27,7 +35,7 @@ Anselm computer provides two main shared filesystems, the [HOME
filesystem](../storage.html#home) and the [SCRATCH
filesystem](../storage.html#scratch). Both HOME and
SCRATCH filesystems are realized as a parallel Lustre filesystem. Both
-shared file systems are ible via the Infiniband network. Extended
+shared file systems are accessible via the Infiniband network. Extended
ACLs are provided on both Lustre filesystems for the purpose of sharing
data with other users using fine-grained control.
@@ -42,7 +50,7 @@ round-robin fashion to ensure load balancing.
When a client (a compute
node from your job) needs to create
-or a file, the client queries the metadata server (
+or access a file, the client queries the metadata server (
MDS) and the metadata target (
MDT) for the layout and location of the
[file's
@@ -81,7 +89,7 @@ significantly impact the I/O performance you experience.
Use the lfs getstripe for getting the stripe parameters. Use the lfs
setstripe command for setting the stripe parameters to get optimal I/O
performance The correct stripe setting depends on your needs and file
- patterns.
+access patterns.
```
$ lfs getstripe dir|filename
@@ -122,7 +130,7 @@ When multiple processes are writing blocks of data to the same file in
parallel, the I/O performance for large files will improve when the
stripe_count is set to a larger value. The stripe count sets the number
of OSTs the file will be written to. By default, the stripe count is set
-to 1. While this default setting provides for efficient of
+to 1. While this default setting provides for efficient access of
metadata (for example to support the ls -l command), large files should
use stripe counts of greater than 1. This will increase the aggregate
I/O bandwidth by using multiple OSTs in parallel instead of just one. A
@@ -134,10 +142,10 @@ of the number of processes performing the write in parallel, so that you
achieve load balance among the OSTs. For example, set the stripe count
to 16 instead of 15 when you have 64 processes performing the writes.
-Using a large stripe size can improve performance when ing very
+Using a large stripe size can improve performance when accessing very
large files
-Large stripe size allows each client to have exclusive to its own
+Large stripe size allows each client to have exclusive access to its own
part of a file. However, it can be counterproductive in some cases if it
does not match your I/O pattern. The choice of stripe size has no effect
on a single-stripe file.
@@ -249,7 +257,7 @@ prove as insufficient for particular user, please contact
lifted upon request.
The Scratch filesystem is intended for temporary scratch data generated
-during the calculation as well as for high performance to input
+during the calculation as well as for high performance access to input
and output files. All I/O intensive jobs must use the SCRATCH filesystem
as their working directory.
@@ -257,7 +265,7 @@ Users are advised to save the necessary data from the SCRATCH filesystem
to HOME filesystem after the calculations and clean up the scratch
files.
-Files on the SCRATCH filesystem that are **not ed for more than 90
+Files on the SCRATCH filesystem that are **not accessed for more than 90
days** will be automatically **deleted**.
The SCRATCH filesystem is realized as Lustre parallel filesystem and is
@@ -370,7 +378,7 @@ number of named user and named group entries.
ACLs on a Lustre file system work exactly like ACLs on any Linux file
system. They are manipulated with the standard tools in the standard
-manner. Below, we create a directory and allow a specific user .
+manner. Below, we create a directory and allow a specific user access.
```
[vop999@login1.anselm ~]$ umask 027
@@ -414,18 +422,18 @@ Local Filesystems
Every computational node is equipped with 330GB local scratch disk.
-Use local scratch in case you need to large amount of small files
+Use local scratch in case you need to access large amount of small files
during your calculation.
-The local scratch disk is mounted as /lscratch and is ible to
+The local scratch disk is mounted as /lscratch and is accessible to
user at /lscratch/$PBS_JOBID directory.
The local scratch filesystem is intended for temporary scratch data
-generated during the calculation as well as for high performance
-to input and output files. All I/O intensive jobs that large
+generated during the calculation as well as for high performance access
+to input and output files. All I/O intensive jobs that access large
number of small files within the calculation must use the local scratch
filesystem as their working directory. This is required for performance
-reasons, as frequent to number of small files may overload the
+reasons, as frequent access to number of small files may overload the
metadata servers (MDS) of the Lustre filesystem.
The local scratch directory /lscratch/$PBS_JOBID will be deleted
@@ -448,16 +456,16 @@ none
Every computational node is equipped with filesystem realized in memory,
so called RAM disk.
-Use RAM disk in case you need really fast to your data of limited
+Use RAM disk in case you need really fast access to your data of limited
size during your calculation.
Be very careful, use of RAM disk filesystem is at the expense of
operational memory.
-The local RAM disk is mounted as /ramdisk and is ible to user
+The local RAM disk is mounted as /ramdisk and is accessible to user
at /ramdisk/$PBS_JOBID directory.
The local RAM disk filesystem is intended for temporary scratch data
-generated during the calculation as well as for high performance
+generated during the calculation as well as for high performance access
to input and output files. Size of RAM disk filesystem is limited. Be
very careful, use of RAM disk filesystem is at the expense of
operational memory. It is not recommended to allocate large amount of
@@ -504,6 +512,14 @@ Mountpoint Usage Protocol
/scratch cluster shared jobs' data Lustre 146 TiB 6 GB/s Quota 100TB Compute and login nodes files older 90 days removed
/lscratch node local jobs' data local 330 GB 100 MB/s none Compute nodes purged after job ends
/ramdisk node local jobs' data local 60, 90, 500 GB 5-50 GB/s none Compute nodes purged after job ends
- /tmp local temporary files local 100 MB/s none Compute and login nodes auto purged
+ /tmp local temporary files local 9.5 GB 100 MB/s none Compute and login nodes auto purged
+
+
+
+
+
+
+
+
diff --git a/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/cygwin-and-x11-forwarding.md b/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/cygwin-and-x11-forwarding.md
index b8c46a60..b4b6cb16 100644
--- a/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/cygwin-and-x11-forwarding.md
+++ b/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/cygwin-and-x11-forwarding.md
@@ -1,6 +1,14 @@
Cygwin and X11 forwarding
=========================
+
+
+
+
+
+
+
+
### If no able to forward X11 using PuTTY to CygwinX
```
@@ -23,17 +31,17 @@ PuTTY X11 proxy: unable to connect to forwarded X server: Network error: Connect
change it
-
+ to</span>
C:*cygwin64binXWin.exe -listen tcp*
- 
+ 
-2. Check Putty settings:
+2.
Check Putty settings:
Enable X11
-
+ forwarding
@@ -43,3 +51,5 @@ PuTTY X11 proxy: unable to connect to forwarded X server: Network error: Connect
+
+
diff --git a/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/graphical-user-interface.md b/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/graphical-user-interface.md
index 454ee5cd..6032500e 100644
--- a/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/graphical-user-interface.md
+++ b/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/graphical-user-interface.md
@@ -5,10 +5,18 @@ Graphical User Interface
+
+
+
+
+
+
+
+
X Window System
---------------
-The X Window system is a principal way to get GUI to the
+The X Window system is a principal way to get GUI access to the
clusters.
Read more about configuring [**X Window
@@ -27,6 +35,8 @@ to remotely control another
class="link-external">[computer](http://en.wikipedia.org/wiki/Computer "Computer").
Read more about configuring
-[VNC](../../../salomon/ing-the-cluster/graphical-user-interface/vnc.html)**.
+**[VNC](../../../salomon/accessing-the-cluster/graphical-user-interface/vnc.html)**.
+
+
diff --git a/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc.md b/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc.md
index fa6db552..4309360c 100644
--- a/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc.md
+++ b/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc.md
@@ -5,6 +5,14 @@ VNC
+
+
+
+
+
+
+
+
The **Virtual Network Computing** (**VNC**) is a graphical [desktop
sharing](http://en.wikipedia.org/wiki/Desktop_sharing "Desktop sharing")
system that uses the [Remote Frame Buffer protocol
@@ -18,7 +26,7 @@ and
events from one computer to another, relaying the graphical
[screen](http://en.wikipedia.org/wiki/Computer_screen "Computer screen")
updates back in the other direction, over a
-[network](http://en.wikipedia.org/wiki/Computer_network "Computer network").(http://en.wikipedia.org/wiki/Virtual_Network_Computing#cite_note-1)^
+[network](http://en.wikipedia.org/wiki/Computer_network "Computer network").(http://en.wikipedia.org/wiki/Virtual_Network_Computing#cite_note-1)
The recommended clients are
[TightVNC](http://www.tightvnc.com) or
@@ -40,13 +48,13 @@ Verify:
Start vncserver
---------------
-To VNC a local vncserver must be started first and also a tunnel
+To access VNC a local vncserver must be started first and also a tunnel
using SSH port forwarding must be established.
[See below](vnc.html#linux-example-of-creating-a-tunnel)
for the details on SSH tunnels. In this example we use port 61.
You can find ports which are already occupied. Here you can see that
-ports "/usr/bin/Xvnc :79" and "
+ports " /usr/bin/Xvnc :79" and "
/usr/bin/Xvnc :60" are occupied.
```
@@ -78,7 +86,7 @@ X DISPLAY # PROCESS ID
:61 18437
```
-Another command:
+Another command:
```
[username@login2 .vnc]$ ps aux | grep Xvnc
@@ -86,7 +94,7 @@ Another command:
username 10296 0.0 0.0 131772 21076 pts/29 SN 13:01 0:01 /usr/bin/Xvnc :61 -desktop login2:61 (username) -auth /home/jir13/.Xauthority -geometry 1600x900 -depth 16 -rfbwait 30000 -rfbauth /home/username/.vnc/passwd -rfbport 5961 -fp catalogue:/etc/X11/fontpath.d -pn
```
-To the VNC server you have to create a tunnel between the login
+To access the VNC server you have to create a tunnel between the login
node using TCP **port 5961** and your machine using a free TCP port (for
simplicity the very same, in this case).
@@ -163,7 +171,7 @@ Fill the Source port and Destination fields. **Do not forget to click
the Add button**.
-tunnel](https://docs.it4i.cz/get-started-with-it4innovations/ing-the-clusters/graphical-user-interface/vnc/putty-tunnel.png/@@images/4c66cd51-c858-473b-98c2-8d901aea7118.png "PuTTY Tunnel")](putty-tunnel.png)
+
Run the VNC client of your choice, select VNC server 127.0.0.1, port
5961 and connect using VNC password.
@@ -199,12 +207,12 @@ You should see after the successful login.
Open Screensaver preferences dialog:
-
+
Uncheck both options below the slider:
-
+
### Kill screensaver if locked screen
@@ -239,7 +247,7 @@ GUI applications on compute nodes over VNC
------------------------------------------
The very [same methods as described
-above](https://docs.it4i.cz/get-started-with-it4innovations/ing-the-clusters/graphical-user-interface/x-window-and-vnc#gui-applications-on-compute-nodes),
+above](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-and-vnc#gui-applications-on-compute-nodes),
may be used to run the GUI applications on compute nodes. However, for
maximum performance**, proceed following these steps:
@@ -277,3 +285,5 @@ Example described above:
+
+
diff --git a/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vpnuiV.png b/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vpnuiV.png
deleted file mode 100644
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zeV?)CyMp)}TXn}@Grq5%cVNBT9${xUm0!h2U+!C8+^fBQca&Gh2IDn5XC|K26<Wk^
z*zn9h<HhzD_xJohb~{V5^WI`rt*&X`#HxjzIP#x{3UMg5fErpY5}#ri((305IB{GI
b|0Dmx*)#m@%nC~e1_lOCS3j3^P6<r_IXo#*
diff --git a/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system.md b/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system.md
index 1f0b4eba..2ce2407a 100644
--- a/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system.md
+++ b/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system.md
@@ -5,7 +5,15 @@ X Window System
-The X Window system is a principal way to get GUI to the
+
+
+
+
+
+
+
+
+The X Window system is a principal way to get GUI access to the
clusters. The **X Window System** (commonly known as **X11**, based on
its current major version being 11, or shortened to simply **X**, and
sometimes informally **X-Windows**) is a computer software system and
@@ -200,3 +208,5 @@ in the local X server
Use System->Log Out to close the gnome-session
+
+
diff --git a/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/introduction.md b/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/introduction.md
index 1bbcf509..baee0ca1 100644
--- a/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/introduction.md
+++ b/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/introduction.md
@@ -1,21 +1,33 @@
Accessing the Clusters
======================
-The IT4Innovations clusters are ed by SSH protocol via login
+
+
+
+
+
+
+
+
+The IT4Innovations clusters are accessed by SSH protocol via login
nodes.
Read more on [Accessing the Salomon
-Cluste](../salomon/ing-the-cluster.html)r or
+Cluste](../salomon/accessing-the-cluster.html)r or
[Accessing the Anselm
-Cluster](../anselm-cluster-documentation/ing-the-cluster.html)
+Cluster](../anselm-cluster-documentation/accessing-the-cluster.html)
pages.
### PuTTY
On **Windows**, use [PuTTY ssh
-client](ing-the-clusters/shell-access-and-data-transfer/putty/putty.html).
+client](accessing-the-clusters/shell-access-and-data-transfer/putty/putty.html).
### SSH keys
Read more about [SSH keys
-management](ing-the-clusters/shell-access-and-data-transfer/ssh-keys.html).
+management](accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.html).
+
+
+
+
diff --git a/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/introduction.md b/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/introduction.md
index cbfc29c5..a5c02508 100644
--- a/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/introduction.md
+++ b/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/introduction.md
@@ -1,13 +1,21 @@
Accessing the Clusters
======================
-The IT4Innovations clusters are ed by SSH protocol via login
+
+
+
+
+
+
+
+
+The IT4Innovations clusters are accessed by SSH protocol via login
nodes.
Read more on [Accessing the Salomon
-Cluste](../../../salomon/ing-the-cluster.html)r or
+Cluste](../../../salomon/accessing-the-cluster.html)r or
[Accessing the Anselm
-Cluster](../../../anselm-cluster-documentation/ing-the-cluster.html)
+Cluster](../../../anselm-cluster-documentation/accessing-the-cluster.html)
pages.
### PuTTY
@@ -18,3 +26,7 @@ client](putty/putty.html).
### SSH keys
Read more about [SSH keys management](ssh-keys.html).
+
+
+
+
diff --git a/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/pageant.md b/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/pageant.md
index 6e004088..17885023 100644
--- a/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/pageant.md
+++ b/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/pageant.md
@@ -5,6 +5,14 @@ Pageant SSH agent
+
+
+
+
+
+
+
+
Pageant holds your private key in memory without needing to retype a
passphrase on every login.
@@ -15,6 +23,10 @@ passphrase on every login.
- Now you have your private key in memory without needing to retype a
passphrase on every login.
- [](PageantV.png)
+ 
+
+
+
+
diff --git a/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty.md b/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty.md
index 72e0950e..7431f8cf 100644
--- a/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty.md
+++ b/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty.md
@@ -5,7 +5,15 @@ PuTTY
-PuTTY - before we start SSH connection ssh-connection style="text-align: start; "}
+
+
+
+
+
+
+
+
+PuTTY - before we start SSH connection
---------------------------------------------------------------------------------
### Windows PuTTY Installer
@@ -41,7 +49,7 @@ PuTTY - how to connect to the IT4Innovations cluster
- Run PuTTY
- Enter Host name and Save session fields with [Login
- address](../../../../salomon/ing-the-cluster/shell-and-data-access/shell-and-data-access.html)
+ address](../../../../salomon/accessing-the-cluster/shell-and-data-access/shell-and-data-access.html)
and browse Connection - > SSH -> Auth menu.
The *Host Name* input may be in the format
**"username@clustername.it4i.cz"** so you don't have to type your
@@ -49,7 +57,7 @@ PuTTY - how to connect to the IT4Innovations cluster
In this example we will connect to the Salomon cluster using
**"salomon.it4i.cz"**.
- [](PuTTY_host_Salomon.png)
+ 
@@ -59,16 +67,16 @@ PuTTY - how to connect to the IT4Innovations cluster
Browse and select your [private
key](../ssh-keys.html) file.
- [](PuTTY_keyV.png)
+ 
- Return to Session page and Save selected configuration with *Save*
button.
- [](PuTTY_save_Salomon.png)
+ 
- Now you can log in using *Open* button.
- [](PuTTY_open_Salomon.png)
+ 
- Enter your username if the *Host Name* input is not in the format
"username@salomon.it4i.cz".
@@ -84,9 +92,13 @@ Another PuTTY Settings
- Category -> Windows -> Translation -> Remote character set
and select **UTF-8**.
-<!-- -->
+
- Category -> Terminal -> Features and select **Disable
application keypad mode** (enable numpad)
- Save your configuration on Session page in to Default Settings with
*Save* button .
+
+
+
+
diff --git a/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/puttygen.md b/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/puttygen.md
index f6e3ea24..cde0d809 100644
--- a/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/puttygen.md
+++ b/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/puttygen.md
@@ -5,6 +5,14 @@ PuTTY key generator
+
+
+
+
+
+
+
+
PuTTYgen is the PuTTY key generator. You can load in an existing private
key and change your passphrase or generate a new public/private key
pair.
@@ -21,7 +29,7 @@ Make sure to backup the key.
- Confirm key passphrase.
- Save your private key with *Save private key* button.
- [](PuttyKeygeneratorV.png)
+ 
@@ -33,15 +41,15 @@ key into authorized_keys file for authentication with your own private
- Start with *Generate* button.
- [](PuttyKeygenerator_001V.png)
+ 
- Generate some randomness.
- [](PuttyKeygenerator_002V.png)
+ 
- Wait.
- [](20150312_143443.png)
+ 
- Enter a *comment* for your key using format
'username@organization.example.com'.
@@ -50,18 +58,18 @@ key into authorized_keys file for authentication with your own private
Save your new private key `in "*.ppk" `format with *Save private
key* button.
- [](PuttyKeygenerator_004V.png)
+ 
- Save the public key with *Save public key* button.
You can copy public key out of the ‘Public key for pasting into
authorized_keys file’ box.
- [](PuttyKeygenerator_005V.png)
+ 
- Export private key in OpenSSH format "id_rsa" using Conversion
-> Export OpenSSH key
- [](PuttyKeygenerator_006V.png)
+ 
- Now you can insert additional public key into authorized_keys file
for authentication with your own private >key.
@@ -69,3 +77,7 @@ key into authorized_keys file for authentication with your own private
proceed to [How to add your own
key](../ssh-keys.html).
+
+
+
+
diff --git a/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.md b/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.md
index 1fafc36c..73979840 100644
--- a/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.md
+++ b/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.md
@@ -5,7 +5,15 @@ SSH keys
-
+
+
+
+
+
+
+
+
+ Key management
-------------------------------------------------------------------
After logging in, you can see .ssh/ directory with SSH keys and
@@ -52,7 +60,7 @@ the cluster.
-<!-- -->
+
cd /home/username/
chmod 700 .ssh/
@@ -70,8 +78,8 @@ The path to a private key is usually /home/username/.ssh/
Private key file in "id_rsa" or `"*.ppk" `format is used to
authenticate with the servers.
Private key is present locally
-on local side and used for example in SSH agent
-. The private key should
+on local side and used for example in SSH agent [Pageant (for Windows
+users)](putty/PageantV.png). The private key should
always be kept in a safe place.
An example of private key
@@ -113,7 +121,7 @@ verify a
digital signature. Public
key is present on the remote
-side and allows to
+side and allows access to
the owner of the matching private key.
An example of public key
diff --git a/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/vpn-connection-fail-in-win-8.1.md b/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/vpn-connection-fail-in-win-8.1.md
index 604bdf27..aa82e6f2 100644
--- a/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/vpn-connection-fail-in-win-8.1.md
+++ b/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/vpn-connection-fail-in-win-8.1.md
@@ -1,7 +1,19 @@
VPN - Connection fail in Win 8.1
================================
+
+
+
+
Failed to initialize connection subsystem Win 8.1 - 02-10-15 MS patch
+
+
+
+
+
+
+
+
AnyConnect users on Windows 8.1 will receive a "Failed to initialize
connection subsystem" error after installing the Windows 8.1 02/10/15
security patch. This OS defect introduced with the 02/10/15 patch update
@@ -9,7 +21,7 @@ will also impact WIndows 7 users with IE11. Windows Server
2008/2012 are also impacted by this defect, but neither is a supported
OS for AnyConnect.
-Workaround:**
+**Workaround:**
- Close the Cisco AnyConnect Window and the taskbar mini-icon
- Right click vpnui.exe in the 'Cisco AnyConnect Secure Mobility
@@ -25,3 +37,5 @@ Workaround:**
+
+
diff --git a/converted/docs.it4i.cz/get-started-with-it4innovations/applying-for-resources.md b/converted/docs.it4i.cz/get-started-with-it4innovations/applying-for-resources.md
index 8b592cb5..17af28e4 100644
--- a/converted/docs.it4i.cz/get-started-with-it4innovations/applying-for-resources.md
+++ b/converted/docs.it4i.cz/get-started-with-it4innovations/applying-for-resources.md
@@ -5,6 +5,14 @@ Applying for Resources
+
+
+
+
+
+
+
+
Computational resources may be allocated by any of the following
[Computing resources
allocation](http://www.it4i.cz/computing-resources-allocation/?lang=en)
@@ -12,7 +20,7 @@ mechanisms.
Academic researchers can apply for computational resources via [Open
Access
-Competitions](http://www.it4i.cz/open--competition/?lang=en&lang=en).
+Competitions](http://www.it4i.cz/open-access-competition/?lang=en&lang=en).
Anyone is welcomed to apply via the [Directors
Discretion.](http://www.it4i.cz/obtaining-computational-resources-through-directors-discretion/?lang=en&lang=en)
@@ -21,7 +29,7 @@ Foreign (mostly European) users can obtain computational resources via
the [PRACE (DECI)
program](http://www.prace-ri.eu/DECI-Projects).
-In all cases, IT4Innovations’ mechanisms are aimed at
+In all cases, IT4Innovations’ access mechanisms are aimed at
distributing computational resources while taking into account the
development and application of supercomputing methods and their benefits
and usefulness for society. The applicants are expected to submit a
@@ -37,3 +45,7 @@ and [Obtaining Login
Credentials](obtaining-login-credentials.html) page.
+
+
+
+
diff --git a/converted/docs.it4i.cz/get-started-with-it4innovations/introduction.md b/converted/docs.it4i.cz/get-started-with-it4innovations/introduction.md
index faec5ef5..b833142f 100644
--- a/converted/docs.it4i.cz/get-started-with-it4innovations/introduction.md
+++ b/converted/docs.it4i.cz/get-started-with-it4innovations/introduction.md
@@ -5,6 +5,14 @@ Documentation
+
+
+
+
+
+
+
+
Welcome to IT4Innovations documentation pages. The IT4Innovations
national supercomputing center operates supercomputers
[Salomon](../salomon.html) and
@@ -15,7 +23,7 @@ industrial community worldwide. The purpose of these pages is to provide
a comprehensive documentation on hardware, software and usage of the
computers.
- class="link-external"> class="WYSIWYG_LINK">How to read the documentation
+ class="link-external">How to read the documentation
--------------------------------------------------------------------------------------------------
1.Read the list in the left column. Select the subject of interest.
@@ -143,3 +151,6 @@ entering the details of your errata. Once your errata are verified, your
submission will be accepted and the errata will be uploaded on our
website.
+
+
+
diff --git a/converted/docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials/certificates-faq.md b/converted/docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials/certificates-faq.md
index 493abbda..92ab874b 100644
--- a/converted/docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials/certificates-faq.md
+++ b/converted/docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials/certificates-faq.md
@@ -1,12 +1,24 @@
Certificates FAQ
================
+
+
+
+
FAQ about certificates in general
+
+
+
+
+
+
+
+
Q: What are certificates?
-------------------------
@@ -20,15 +32,15 @@ of use. We mention here:
- User (Private) certificates
-<!-- -->
+
- Certificate Authority (CA) certificates
-<!-- -->
+
- Host certificates
-<!-- -->
+
- Service certificates
@@ -222,7 +234,7 @@ where $mydomain.crt is the certificate of a trusted signing authority
More information on the tool can be found
at:<http://docs.oracle.com/javase/7/docs/technotes/tools/solaris/keytool.html>
-Q: How do I use my certificate to the different grid Services?
+Q: How do I use my certificate to access the different grid Services?
---------------------------------------------------------------------
Most grid services require the use of your certificate; however, the
@@ -237,7 +249,7 @@ If the grid service is UNICORE, then you bind your certificate, in
either the p12 format or JKS, to UNICORE during the installation of the
client on your local machine. For more information, please visit
[UNICORE6 in PRACE](http://www.prace-ri.eu/UNICORE6-in-PRACE){.spip_in
-.external-link}
+.external
If the grid service is part of Globus, such as GSI-SSH, GriFTP or GRAM5,
then the certificates can be in either p12 or PEM format and must reside
@@ -294,7 +306,7 @@ Q: What is the MyProxy service?
-------------------------------
[The MyProxy Service](http://grid.ncsa.illinois.edu/myproxy/){.spip_in
-.external-link}, can be employed by gsissh-term and Globus tools, and is
+.external, can be employed by gsissh-term and Globus tools, and is
an online repository that allows users to store long lived proxy
certificates remotely, which can then be retrieved for use at a later
date. Each proxy is protected by a password provided by the user at the
@@ -303,7 +315,7 @@ to carry their private keys and certificates when travelling; nor do
users have to install private keys and certificates on possibly insecure
computers.
-Q: Someone may have copied or had to the private key of my certificate either in a separate file or in the browser. What should I do?
+Q: Someone may have copied or had access to the private key of my certificate either in a separate file or in the browser. What should I do?
--------------------------------------------------------------------------------------------------------------------------------------------
Please ask the CA that issued your certificate to revoke this certifcate
@@ -313,3 +325,6 @@ team](https://support.it4i.cz/rt).
+
+
+
diff --git a/converted/docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials.md b/converted/docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials.md
index 82b0df2d..5748f4f7 100644
--- a/converted/docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials.md
+++ b/converted/docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials.md
@@ -5,36 +5,44 @@ Obtaining Login Credentials
+
+
+
+
+
+
+
+
Obtaining Authorization
-----------------------
The computational resources of IT4I are allocated by the Allocation
Committee to a [Project](../introduction.html),
investigated by a Primary Investigator. By allocating the computational
-resources, the Allocation Committee is authorizing the PI to and
+resources, the Allocation Committee is authorizing the PI to access and
use the clusters. The PI may decide to authorize a number of her/his
-Collaborators to and use the clusters, to consume the resources
+Collaborators to access and use the clusters, to consume the resources
allocated to her/his Project. These collaborators will be associated to
the Project. The Figure below is depicting the authorization chain:
-
+
You need to either [become the
PI](../applying-for-resources.html) or [be named as a
collaborator](obtaining-login-credentials.html#authorization-of-collaborator-by-pi)
-by a PI in order to and use the clusters.
+by a PI in order to access and use the clusters.
Head of Supercomputing Services acts as a PI of a project DD-13-5.
-Joining this project, you may ** and explore the clusters**, use
+Joining this project, you may **access and explore the clusters**, use
software, development environment and computers via the qexp and qfree
queues. You may use these resources for own education/research, no
paperwork is required. All IT4I employees may contact the Head of
-Supercomputing Services in order to obtain **free to the
+Supercomputing Services in order to obtain **free access to the
clusters**.
### Authorization of PI by Allocation Committee
@@ -45,7 +53,7 @@ the Allocation Committee decision.
### Authorization by web
-This is a preferred way of granting to project resources.
+This is a preferred way of granting access to project resources.
Please, use this method whenever it's possible.
Log in to the [IT4I Extranet
@@ -69,7 +77,7 @@ following information:
2.Provide list of people, including himself, who are authorized to use
the resources allocated to the project. The list must include full
name, e-mail and affiliation. Provide usernames as well, if
- collaborator login already exists on the IT4I systems.
+ collaborator login access already exists on the IT4I systems.
3.Include "Authorization to IT4Innovations" into the subject line.
Example (except the subject line which must be in English, you may use
@@ -98,7 +106,7 @@ The Login Credentials
-------------------------
Once authorized by PI, every person (PI or Collaborator) wishing to
- the clusters, should contact the [IT4I
+access the clusters, should contact the [IT4I
support](https://support.it4i.cz/rt/) (E-mail: [support
[at] it4i.cz](mailto:support%20%5Bat%5D%20it4i.cz)) providing
following information:
@@ -144,7 +152,7 @@ Digital signature allows us to confirm your identity in remote
electronic communication and provides an encrypted channel to exchange
sensitive information such as login credentials. After receiving your
signed e-mail with the requested information, we will send you your
-login credentials (user name, key, passphrase and password) to
+login credentials (user name, key, passphrase and password) to access
the IT4I systems.
We accept certificates issued by any widely respected certification
@@ -160,8 +168,8 @@ The login credentials include:
2.ssh private key and private key passphrase
3.system password
-The clusters are ed by the [private
-key](../ing-the-clusters/shell-access-and-data-transfer/ssh-keys.html)
+The clusters are accessed by the [private
+key](../accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.html)
and username.
Username and password is used for login to the information systems
listed on <http://support.it4i.cz/>.
@@ -175,7 +183,7 @@ local $ ssh-keygen -f id_rsa -p
```
On Windows, use [PuTTY Key
-Generator](../ing-the-clusters/shell-access-and-data-transfer/putty/puttygen.html).
+Generator](../accessing-the-clusters/shell-access-and-data-transfer/putty/puttygen.html).
### Change Password
@@ -270,3 +278,7 @@ pending removal:.
The messages will inform about the projected removal date and will
challenge the user to migrate her/his data
+
+
+
+
diff --git a/converted/docs.it4i.cz/index.md b/converted/docs.it4i.cz/index.md
index 42a6d692..682b5b57 100644
--- a/converted/docs.it4i.cz/index.md
+++ b/converted/docs.it4i.cz/index.md
@@ -5,6 +5,14 @@ Documentation
+
+
+
+
+
+
+
+
Welcome to IT4Innovations documentation pages. The IT4Innovations
national supercomputing center operates supercomputers
[Salomon](salomon.html) and
@@ -15,7 +23,7 @@ industrial community worldwide. The purpose of these pages is to provide
a comprehensive documentation on hardware, software and usage of the
computers.
- class="link-external"> class="WYSIWYG_LINK">How to read the documentation
+ class="link-external">How to read the documentation
--------------------------------------------------------------------------------------------------
1.Read the list in the left column. Select the subject of interest.
@@ -143,3 +151,7 @@ them by visiting http://support.it4i.cz/rt, creating a new ticket, and
entering the details of your errata. Once your errata are verified, your
submission will be accepted and the errata will be uploaded on our
website.
+
+
+
+
diff --git a/converted/docs.it4i.cz/salomon/accessing-the-cluster.md b/converted/docs.it4i.cz/salomon/accessing-the-cluster.md
index ecd7e8a6..b7ad64be 100644
--- a/converted/docs.it4i.cz/salomon/accessing-the-cluster.md
+++ b/converted/docs.it4i.cz/salomon/accessing-the-cluster.md
@@ -1,14 +1,22 @@
-Shell and data transfer
+Shell access and data transfer
==============================
+
+
+
+
+
+
+
+
Interactive Login
-----------------
-The Salomon cluster is ed by SSH protocol via login nodes login1,
+The Salomon cluster is accessed by SSH protocol via login nodes login1,
login2, login3 and login4 at address salomon.it4i.cz. The login nodes
may be addressed specifically, by prepending the login node name to the
address.
@@ -26,7 +34,7 @@ login3.salomon.it4i.cz 22 ssh login3
login4.salomon.it4i.cz 22 ssh login4
The authentication is by the [private
-key](../get-started-with-it4innovations/ing-the-clusters/shell-access-and-data-transfer/ssh-keys.html)
+key](../get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.html)
Please verify SSH fingerprints during the first logon. They are
identical on all login nodes:
@@ -51,7 +59,7 @@ local $ chmod 600 /path/to/id_rsa
```
On **Windows**, use [PuTTY ssh
-client](../get-started-with-it4innovations/ing-the-clusters/shell-access-and-data-transfer/putty/putty.html).
+client](../get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/putty.html).
After logging in, you will see the command prompt:
@@ -91,11 +99,11 @@ Address Port Protocol
salomon.it4i.cz 22 scp, sftp
login1.salomon.it4i.cz 22 scp, sftp
login2.salomon.it4i.cz 22 scp, sftp
- class="discreet">login3.salomon.it4i.cz 22 class="discreet">scp, sftp
+ class="discreet">login3.salomon.it4i.cz 22 scp, sftp
login4.salomon.it4i.cz 22 scp, sftp
The authentication is by the [private
-key](../get-started-with-it4innovations/ing-the-clusters/shell-access-and-data-transfer/ssh-keys.html)
+key](../get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.html)
HTML commented section #2 (ssh transfer performance data need to be
verified)
@@ -143,3 +151,7 @@ way to mount the Salomon filesystems directly as an external disc.
More information about the shared file systems is available
[here](storage/storage.html).
+
+
+
+
diff --git a/converted/docs.it4i.cz/salomon/accessing-the-cluster/outgoing-connections.md b/converted/docs.it4i.cz/salomon/accessing-the-cluster/outgoing-connections.md
index 8d1d5110..4e538c6b 100644
--- a/converted/docs.it4i.cz/salomon/accessing-the-cluster/outgoing-connections.md
+++ b/converted/docs.it4i.cz/salomon/accessing-the-cluster/outgoing-connections.md
@@ -5,6 +5,14 @@ Outgoing connections
+
+
+
+
+
+
+
+
Connection restrictions
-----------------------
@@ -44,7 +52,7 @@ local $ ssh -R 6000:remote.host.com:1234 salomon.it4i.cz
```
In this example, we establish port forwarding between port 6000 on
-Salomon and port 1234 on the remote.host.com. By ing
+Salomon and port 1234 on the remote.host.com. By accessing
localhost:6000 on Salomon, an application will see response of
remote.host.com:1234. The traffic will run via users local workstation.
@@ -55,7 +63,7 @@ Remote radio button. Insert 6000 to Source port textbox. Insert
remote.host.com:1234. Click Add button, then Open.
Port forwarding may be established directly to the remote host. However,
-this requires that user has ssh to remote.host.com
+this requires that user has ssh access to remote.host.com
```
$ ssh -L 6000:localhost:1234 remote.host.com
@@ -66,7 +74,7 @@ Note: Port number 6000 is chosen as an example only. Pick any free port.
### Port forwarding from compute nodes
Remote port forwarding from compute nodes allows applications running on
-the compute nodes to hosts outside Salomon Cluster.
+the compute nodes to access hosts outside Salomon Cluster.
First, establish the remote port forwarding form the login node, as
[described
@@ -80,7 +88,7 @@ $ ssh -TN -f -L 6000:localhost:6000 login1
```
In this example, we assume that port forwarding from login1:6000 to
-remote.host.com:1234 has been established beforehand. By ing
+remote.host.com:1234 has been established beforehand. By accessing
localhost:6000, an application running on a compute node will see
response of remote.host.com:1234
@@ -90,7 +98,7 @@ Port forwarding is static, each single port is mapped to a particular
port on remote host. Connection to other remote host, requires new
forward.
-Applications with inbuilt proxy support, experience unlimited to
+Applications with inbuilt proxy support, experience unlimited access to
remote hosts, via single proxy server.
To establish local proxy server on your workstation, install and run
@@ -114,7 +122,7 @@ local $ ssh -R 6000:localhost:1080 salomon.it4i.cz
```
Now, configure the applications proxy settings to **localhost:6000**.
-Use port forwarding to the [proxy server from compute
+Use port forwarding to access the [proxy server from compute
nodes](outgoing-connections.html#port-forwarding-from-compute-nodes)
as well .
diff --git a/converted/docs.it4i.cz/salomon/accessing-the-cluster/vpn-access.md b/converted/docs.it4i.cz/salomon/accessing-the-cluster/vpn-access.md
index b12c1d76..3a0b5b8d 100644
--- a/converted/docs.it4i.cz/salomon/accessing-the-cluster/vpn-access.md
+++ b/converted/docs.it4i.cz/salomon/accessing-the-cluster/vpn-access.md
@@ -5,6 +5,14 @@ VPN Access
+
+
+
+
+
+
+
+
Accessing IT4Innovations internal resources via VPN
---------------------------------------------------
@@ -40,7 +48,7 @@ for automatic installation.
-
+Install](https://docs.it4i.cz/salomon/vpn_web_install_2.png/@@images/c2baba93-824b-418d-b548-a73af8030320.png "VPN Install")](../vpn_web_install_2.png)
After successful installation, VPN connection will be established and
@@ -92,7 +100,7 @@ If everything works, you can see a lock in the Cisco tray icon.
If you right-click on this icon, you will see a context menu in which
you can control the VPN connection.
-
+[
When you connect to the VPN for the first time, the client downloads the
@@ -101,18 +109,18 @@ For subsequent connections, it is not necessary to re-enter the URL
address, but just select the corresponding item.
Contacting
-
+
Then AnyConnect automatically proceeds like in the case of first logon.
-
+
After a successful logon, you can see a green circle with a tick mark on
the lock icon.
Succesfull
-
+
For disconnecting, right-click on the AnyConnect client icon in the
system tray and select **VPN Disconnect**.
diff --git a/converted/docs.it4i.cz/salomon/environment-and-modules.md b/converted/docs.it4i.cz/salomon/environment-and-modules.md
index b8323d2f..525d2a9d 100644
--- a/converted/docs.it4i.cz/salomon/environment-and-modules.md
+++ b/converted/docs.it4i.cz/salomon/environment-and-modules.md
@@ -5,6 +5,14 @@ Environment and Modules
+
+
+
+
+
+
+
+
### Environment Customization
After logging in, you may want to configure the environment. Write your
@@ -34,7 +42,7 @@ Do not run commands outputing to standard output (echo, module list,
etc) in .bashrc for non-interactive SSH sessions. It breaks fundamental
functionality (scp, PBS) of your account! Take care for SSH session
interactivity for such commands as id="result_box"
-class="short_text"> class="hps alt-edited">stated
+ class="hps alt-edited">stated
in the previous example.
### Application Modules
@@ -131,7 +139,7 @@ The EasyBuild framework prepares the build environment for the different
toolchain components, by loading their respective modules and defining
environment variables to specify compiler commands (e.g.,
via `$F90`), compiler and linker options (e.g.,
-via `$CFLAGS` and `$LDFLAGS`),
+via `$CFLAGS` and `$LDFLAGS`{.docutils .literal}),
the list of library names to supply to the linker (via `$LIBS`{.docutils
.literal}), etc. This enables making easyblocks
largely toolchain-agnostic since they can simply rely on these
@@ -162,3 +170,5 @@ goolf BLACS, FFTW, GCC, OpenBLAS, OpenMPI, ScaLAPACK
iccifort icc, ifort
+
+
diff --git a/converted/docs.it4i.cz/salomon/hardware-overview-1/hardware-overview.md b/converted/docs.it4i.cz/salomon/hardware-overview-1/hardware-overview.md
index 9f246a4c..58e4577f 100644
--- a/converted/docs.it4i.cz/salomon/hardware-overview-1/hardware-overview.md
+++ b/converted/docs.it4i.cz/salomon/hardware-overview-1/hardware-overview.md
@@ -5,6 +5,14 @@ Hardware Overview
+
+
+
+
+
+
+
+
Introduction
------------
@@ -15,7 +23,7 @@ with 24 cores (two twelve-core Intel Xeon processors) and 128GB RAM. The
nodes are interlinked by high speed InfiniBand and Ethernet networks.
All nodes share 0.5PB /home NFS disk storage to store the user files.
Users may use a DDN Lustre shared storage with capacity of 1.69 PB which
-is available for the scratch project data. The user to the
+is available for the scratch project data. The user access to the
Salomon cluster is provided by four login nodes.
[More about schematic representation of the Salomon cluster compute
@@ -23,7 +31,7 @@ nodes IB
topology](../network-1/ib-single-plane-topology.html).
-
+
The parameters are summarized in the following tables:
@@ -121,3 +129,6 @@ available:
+
+
+
diff --git a/converted/docs.it4i.cz/salomon/index.md b/converted/docs.it4i.cz/salomon/index.md
index 90a83ecd..1d945a17 100644
--- a/converted/docs.it4i.cz/salomon/index.md
+++ b/converted/docs.it4i.cz/salomon/index.md
@@ -1,6 +1,14 @@
Introduction
============
+
+
+
+
+
+
+
+
Welcome to Salomon supercomputer cluster. The Salomon cluster consists
of 1008 compute nodes, totaling 24192 compute cores with 129TB RAM and
giving over 2 Pflop/s theoretical peak performance. Each node is a
@@ -19,15 +27,18 @@ the class="WYSIWYG_LINK">RedHat [
class="WYSIWYG_LINK">Linux
family.](http://upload.wikimedia.org/wikipedia/commons/1/1b/Linux_Distribution_Timeline.svg)
-**Water-cooled Compute Nodes With MIC Accelerator**
-
+Water-cooled Compute Nodes With MIC Accelerator**
+[](salomon)
-
+
**Tape Library T950B**
-
+
+
+
+
+
-
diff --git a/converted/docs.it4i.cz/salomon/introduction.md b/converted/docs.it4i.cz/salomon/introduction.md
index 90a83ecd..820bd868 100644
--- a/converted/docs.it4i.cz/salomon/introduction.md
+++ b/converted/docs.it4i.cz/salomon/introduction.md
@@ -1,6 +1,14 @@
Introduction
============
+
+
+
+
+
+
+
+
Welcome to Salomon supercomputer cluster. The Salomon cluster consists
of 1008 compute nodes, totaling 24192 compute cores with 129TB RAM and
giving over 2 Pflop/s theoretical peak performance. Each node is a
@@ -19,9 +27,9 @@ the class="WYSIWYG_LINK">RedHat [
class="WYSIWYG_LINK">Linux
family.](http://upload.wikimedia.org/wikipedia/commons/1/1b/Linux_Distribution_Timeline.svg)
-**Water-cooled Compute Nodes With MIC Accelerator**
-
+Water-cooled Compute Nodes With MIC Accelerator**
+
@@ -31,3 +39,6 @@ family.](http://upload.wikimedia.org/wikipedia/commons/1/1b/Linux_Distribution_T
+
+
+
diff --git a/converted/docs.it4i.cz/salomon/network-1/7d-enhanced-hypercube.md b/converted/docs.it4i.cz/salomon/network-1/7d-enhanced-hypercube.md
index 9487e731..f676804e 100644
--- a/converted/docs.it4i.cz/salomon/network-1/7d-enhanced-hypercube.md
+++ b/converted/docs.it4i.cz/salomon/network-1/7d-enhanced-hypercube.md
@@ -1,6 +1,14 @@
7D Enhanced Hypercube
=====================
+
+
+
+
+
+
+
+
[More about Job submission - Placement by IB switch / Hypercube
dimension.](../resource-allocation-and-job-execution/job-submission-and-execution.html)
@@ -20,7 +28,7 @@ Hypercube dimension
topology represents hypercube
dimension 0](ib-single-plane-topology.html).
-### 7D Enhanced Hypercube
+### 7D Enhanced Hypercube {#d-enhanced-hypercube}
@@ -33,8 +41,8 @@ compute nodes MIC accelerated 432 cns577 - cns1008 r21u01n577 - r
### IB Topology
-
-
+ [](Salomon_IB_topology.png)
diff --git a/converted/docs.it4i.cz/salomon/network-1/ib-single-plane-topology.md b/converted/docs.it4i.cz/salomon/network-1/ib-single-plane-topology.md
index 7e585bd3..25f628f3 100644
--- a/converted/docs.it4i.cz/salomon/network-1/ib-single-plane-topology.md
+++ b/converted/docs.it4i.cz/salomon/network-1/ib-single-plane-topology.md
@@ -5,6 +5,14 @@ IB single-plane topology
+
+
+
+
+
+
+
+
A complete M-Cell assembly consists of four compute racks. Each rack
contains 4x physical IRUs - Independent rack units. Using one dual
socket node per one blade slot leads to 8 logical IRUs. Each rack
@@ -24,7 +32,7 @@ with connections as follows:
Each colour in each physical IRU represents one dual-switch ASIC switch.
-[](https://docs.it4i.cz/salomon/network-1/ib-single-plane-topology/IB%20single-plane%20topology%20-%20ICEX%20Mcell.pdf)
+
@@ -42,10 +50,11 @@ Topology](Salomon_IB_topology.png):
- Racks 27, 28, 29, 30, 31, 32 are equivalent to one Mcell rack.
- Racks 33, 34, 35, 36, 37, 38 are equivalent to one Mcell rack.
-[](https://docs.it4i.cz/salomon/network-1/ib-single-plane-topology/IB%20single-plane%20topology%20-%20Accelerated%20nodes.pdf)
+
+
+
diff --git a/converted/docs.it4i.cz/salomon/network-1/network.md b/converted/docs.it4i.cz/salomon/network-1/network.md
index 235fb38c..56d876fc 100644
--- a/converted/docs.it4i.cz/salomon/network-1/network.md
+++ b/converted/docs.it4i.cz/salomon/network-1/network.md
@@ -5,6 +5,14 @@ Network
+
+
+
+
+
+
+
+
All compute and login nodes of Salomon are interconnected by 7D Enhanced
hypercube
[Infiniband](http://en.wikipedia.org/wiki/InfiniBand)
@@ -27,11 +35,11 @@ Read more about schematic representation of the Salomon cluster [IB
single-plain topology](ib-single-plane-topology.html)
([hypercube dimension](7d-enhanced-hypercube.html)
0).[>](IB%20single-plane%20topology%20-%20Accelerated%20nodes.pdf/view.html){.state-missing-value
+.contenttype-file}
-
-The compute nodes may be ed via the Infiniband network using ib0
+The compute nodes may be accessed via the Infiniband network using ib0
network interface, in address range 10.17.0.0 (mask 255.255.224.0). The
MPI may be used to establish native Infiniband connection among the
nodes.
@@ -54,7 +62,7 @@ Job ID Username Queue Jobname SessID NDS TSK Memory Time S Time
r4i1n0/0*24+r4i1n1/0*24+r4i1n2/0*24+r4i1n3/0*24
```
-In this example, we the node r4i1n0 by Infiniband network via the
+In this example, we access the node r4i1n0 by Infiniband network via the
ib0 interface.
```
@@ -79,3 +87,4 @@ inet 10.17.35.19....
+
diff --git a/converted/docs.it4i.cz/salomon/prace.md b/converted/docs.it4i.cz/salomon/prace.md
index d2f8a2ad..2f165559 100644
--- a/converted/docs.it4i.cz/salomon/prace.md
+++ b/converted/docs.it4i.cz/salomon/prace.md
@@ -5,6 +5,14 @@ PRACE User Support
+
+
+
+
+
+
+
+
Intro
-----
@@ -14,12 +22,12 @@ general documentation applies to them as well. This section shows the
main differences for quicker orientation, but often uses references to
the original documentation. PRACE users who don't undergo the full
procedure (including signing the IT4I AuP on top of the PRACE AuP) will
-not have a password and thus to some services intended for
+not have a password and thus access to some services intended for
regular users. This can lower their comfort, but otherwise they should
be able to use the TIER-1 system as intended. Please see the [Obtaining
Login Credentials
section](../get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials.html),
-if the same level of is required.
+if the same level of access is required.
All general [PRACE User
Documentation](http://www.prace-ri.eu/user-documentation/)
@@ -35,7 +43,7 @@ Helpdesk](http://www.prace-ri.eu/helpdesk-guide264/).
Information about the local services are provided in the [introduction
of general user documentation](introduction.html).
Please keep in mind, that standard PRACE accounts don't have a password
-to the web interface of the local (IT4Innovations) request
+to access the web interface of the local (IT4Innovations) request
tracker and thus a new ticket should be created by sending an e-mail to
support[at]it4i.cz.
@@ -59,7 +67,7 @@ Accessing the cluster
### Access with GSI-SSH
-For all PRACE users the method for interactive (login) and data
+For all PRACE users the method for interactive access (login) and data
transfer based on grid services from Globus Toolkit (GSI SSH and
GridFTP) is supported.
@@ -67,14 +75,14 @@ The user will need a valid certificate and to be present in the PRACE
LDAP (please contact your HOME SITE or the primary investigator of your
project for LDAP account creation).
-Most of the information needed by PRACE users ing the Salomon
+Most of the information needed by PRACE users accessing the Salomon
TIER-1 system can be found here:
- [General user's
FAQ](http://www.prace-ri.eu/Users-General-FAQs)
- [Certificates
FAQ](http://www.prace-ri.eu/Certificates-FAQ)
-- [Interactive using
+- [Interactive access using
GSISSH](http://www.prace-ri.eu/Interactive-Access-Using-gsissh)
- [Data transfer with
GridFTP](http://www.prace-ri.eu/Data-Transfer-with-GridFTP-Details)
@@ -95,9 +103,9 @@ valid 12 hours), use:
-To Salomon cluster, two login nodes running GSI SSH service are
+To access Salomon cluster, two login nodes running GSI SSH service are
available. The service is available from public Internet as well as from
-the internal PRACE network (ible only from other PRACE partners).
+the internal PRACE network (accessible only from other PRACE partners).
Access from PRACE network:**
@@ -166,13 +174,13 @@ gsiscp can be used:
If the user needs to run X11 based graphical application and does not
have a X11 server, the applications can be run using VNC service. If the
-user is using regular SSH based , please see the [section in
+user is using regular SSH based access, please see the [section in
general
-documentation](../get-started-with-it4innovations/ing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html).
+documentation](../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html).
-If the user uses GSI SSH based , then the procedure is similar to
-the SSH based ([look
-here](../get-started-with-it4innovations/ing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html)),
+If the user uses GSI SSH based access, then the procedure is similar to
+the SSH based access ([look
+here](../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html)),
only the port forwarding must be done using GSI SSH:
$ gsissh -p 2222 salomon.it4i.cz -L 5961:localhost:5961
@@ -180,10 +188,10 @@ only the port forwarding must be done using GSI SSH:
### Access with SSH
After successful obtainment of login credentials for the local
-IT4Innovations account, the PRACE users can the cluster as
+IT4Innovations account, the PRACE users can access the cluster as
regular users using SSH. For more information please see the [section in
general
-documentation](ing-the-cluster/shell-and-data-access/shell-and-data-access.html).
+documentation](accessing-the-cluster/shell-and-data-access/shell-and-data-access.html).
File transfers
------------------
@@ -191,12 +199,12 @@ File transfers
PRACE users can use the same transfer mechanisms as regular users (if
they've undergone the full registration procedure). For information
about this, please see [the section in the general
-documentation](ing-the-cluster/shell-and-data-access/shell-and-data-access.html).
+documentation](accessing-the-cluster/shell-and-data-access/shell-and-data-access.html).
Apart from the standard mechanisms, for PRACE users to transfer data
to/from Salomon cluster, a GridFTP server running Globus Toolkit GridFTP
service is available. The service is available from public Internet as
-well as from the internal PRACE network (ible only from other
+well as from the internal PRACE network (accessible only from other
PRACE partners).
There's one control server and three backend servers for striping and/or
@@ -280,8 +288,8 @@ Usage of the cluster
--------------------
There are some limitations for PRACE user when using the cluster. By
-default PRACE users aren't allowed to special queues in the PBS
-Pro to have high priority or exclusive to some special equipment
+default PRACE users aren't allowed to access special queues in the PBS
+Pro to have high priority or exclusive access to some special equipment
like accelerated nodes and high memory (fat) nodes. There may be also
restrictions obtaining a working license for the commercial software
installed on the cluster, mostly because of the license agreement or
@@ -387,3 +395,4 @@ increase.
+
diff --git a/converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/capacity-computing.md b/converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/capacity-computing.md
index 924cfbef..3b559fa7 100644
--- a/converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/capacity-computing.md
+++ b/converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/capacity-computing.md
@@ -5,6 +5,14 @@ Capacity computing
+
+
+
+
+
+
+
+
Introduction
------------
diff --git a/converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/introduction.md b/converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/introduction.md
index 08c8e415..79011dfa 100644
--- a/converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/introduction.md
+++ b/converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/introduction.md
@@ -5,6 +5,14 @@ Resource Allocation and Job Execution
+
+
+
+
+
+
+
+
To run a [job](job-submission-and-execution.html),
[computational
resources](resources-allocation-policy.html) for this
@@ -23,8 +31,8 @@ The resources are allocated to the job in a fairshare fashion, subject
to constraints set by the queue and resources available to the Project.
[The Fairshare](job-priority.html) at Salomon ensures
that individual users may consume approximately equal amount of
-resources per week. The resources are ible via several queues for
-queueing the jobs. The queues provide prioritized and exclusive
+resources per week. The resources are accessible via several queues for
+queueing the jobs. The queues provide prioritized and exclusive access
to the computational resources. Following queues are available to Anselm
users:
@@ -32,7 +40,7 @@ users:
- **qprod**, the Production queue****
- **qlong**, the Long queue
- **qmpp**, the Massively parallel queue
-- **qfat**, the queue to SMP UV2000 machine
+- **qfat**, the queue to access SMP UV2000 machine
- **qfree,** the Free resource utilization queue
Check the queue status at <https://extranet.it4i.cz/rsweb/salomon/>
@@ -60,3 +68,5 @@ HTML commented section #1 (removed Capacity computing section, this
will be optimized for Salomon)
+
+
diff --git a/converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-priority.md b/converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-priority.md
index 0a0caaec..ed77a237 100644
--- a/converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-priority.md
+++ b/converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-priority.md
@@ -1,6 +1,14 @@
Job scheduling
==============
+
+
+
+
+
+
+
+
Job execution priority
----------------------
@@ -39,7 +47,7 @@ Fairshare priority is used for ranking jobs with equal queue priority.
Fairshare priority is calculated as
-
+
where MAX_FAIRSHARE has value 1E6,
usage~Project~ is cumulated usage by all members of selected project,
@@ -75,7 +83,7 @@ job.
Job execution priority (job sort formula) is calculated as:
-
+
### Job backfilling
@@ -109,3 +117,6 @@ walltime could be backfilled - and overtake job(s) with higher priority.
Job [placement can be controlled by flags during
submission](job-submission-and-execution.html#job_placement).
+
+
+
diff --git a/converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-submission-and-execution.md b/converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-submission-and-execution.md
index d0af553e..fc8dc93f 100644
--- a/converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-submission-and-execution.md
+++ b/converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-submission-and-execution.md
@@ -5,6 +5,14 @@ Job submission and execution
+
+
+
+
+
+
+
+
Job Submission
--------------
@@ -90,7 +98,7 @@ approach through attributes "accelerator", "naccelerators" and
"accelerator_model" is used. The "accelerator_model" can be omitted,
since on Salomon only one type of accelerator type/model is available.
-The absence of specialized queue for ing the nodes with cards
+The absence of specialized queue for accessing the nodes with cards
means, that the Phi cards can be utilized in any queue, including qexp
for testing/experiments, qlong for longer jobs, qfree after the project
resources have been spent, etc. The Phi cards are thus also available to
@@ -226,8 +234,16 @@ efficient network communication.
+
+
+
+
There are at most 9 nodes sharing the same Infiniband switch.
+
+
+
+
Infiniband switch list:
@@ -257,6 +273,10 @@ set node r37u32n970 resources_available.switch = r36sw3
set node r37u33n971 resources_available.switch = r36sw3
set node r37u34n972 resources_available.switch = r36sw3
```
+
+
+
+
Nodes sharing the same switch may be selected via the PBS resource
attribute switch.
@@ -274,13 +294,25 @@ $ qsub -A OPEN-0-0 -q qprod -l select=9:ncpus=24:switch=r4i1s0sw1 ./myjob
In this example, we request all the 9 nodes sharing the r4i1s0sw1 switch
for 24 hours.
+
+
+
+
```
$ qsub -A OPEN-0-0 -q qprod -l select=9:ncpus=24 -l place=group=switch ./myjob
```
+
+
+
+
In this example, we request 9 nodes placed on the same switch using node
grouping placement for 24 hours.
+
+
+
+
HTML commented section #1 (turbo boost is to be implemented)
Job Management
@@ -447,11 +479,11 @@ $ pwd
In this example, 4 nodes were allocated interactively for 1 hour via the
qexp queue. The interactive shell is executed in the home directory.
-All nodes within the allocation may be ed via ssh. Unallocated
-nodes are not ible to user.
+All nodes within the allocation may be accessed via ssh. Unallocated
+nodes are not accessible to user.
-The allocated nodes are ible via ssh from login nodes. The nodes
-may each other via ssh as well.
+The allocated nodes are accessible via ssh from login nodes. The nodes
+may access each other via ssh as well.
Calculations on allocated nodes may be executed remotely via the MPI,
ssh, pdsh or clush. You may find out which nodes belong to the
@@ -614,3 +646,5 @@ may use threads.
HTML commented section #3 (Capacity computing need to be reworked)
+
+
diff --git a/converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/resources-allocation-policy.md b/converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/resources-allocation-policy.md
index 0281059a..685681fd 100644
--- a/converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/resources-allocation-policy.md
+++ b/converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/resources-allocation-policy.md
@@ -5,6 +5,14 @@ Resources Allocation Policy
+
+
+
+
+
+
+
+
Resources Allocation Policy
---------------------------
@@ -13,8 +21,8 @@ to constraints set by the queue and resources available to the Project.
The Fairshare at Anselm ensures that individual users may consume
approximately equal amount of resources per week. Detailed information
in the [Job scheduling](job-priority.html) section. The
-resources are ible via several queues for queueing the jobs. The
-queues provide prioritized and exclusive to the computational
+resources are accessible via several queues for queueing the jobs. The
+queues provide prioritized and exclusive access to the computational
resources. Following table provides the queue partitioning overview:
@@ -148,14 +156,14 @@ is allowed after request for this queue.
- **qprod**, the Production queue****: This queue is intended for
normal production runs. It is required that active project with
nonzero remaining resources is specified to enter the qprod. All
- nodes may be ed via the qprod queue, however only 86 per job.
+ nodes may be accessed via the qprod queue, however only 86 per job.
** Full nodes, 24 cores per node are allocated. The queue runs with
medium priority and no special authorization is required to use it.
The maximum runtime in qprod is 48 hours.
- **qlong**, the Long queue****: This queue is intended for long
production runs. It is required that active project with nonzero
remaining resources is specified to enter the qlong. Only 336 nodes
- without acceleration may be ed via the qlong queue. Full
+ without acceleration may be accessed via the qlong queue. Full
nodes, 24 cores per node are allocated. The queue runs with medium
priority and no special authorization is required to use it.>
*The maximum runtime in qlong is 144 hours (three times of the
@@ -163,7 +171,7 @@ is allowed after request for this queue.
- >****qmpp**, the massively parallel queue. This queue is
intended for massively parallel runs. It is required that active
project with nonzero remaining resources is specified to enter
- the qmpp. All nodes may be ed via the qmpp queue. ** Full
+ the qmpp. All nodes may be accessed via the qmpp queue. ** Full
nodes, 24 cores per node are allocated. The queue runs with medium
priority and no special authorization is required to use it. The
maximum runtime in qmpp is 4 hours. An PI> *needs explicitly*
@@ -172,7 +180,7 @@ is allowed after request for this queue.
her/his Project.
- >****qfat**, the UV2000 queue. This queue is dedicated
- to the fat SGI UV2000 SMP machine. The machine (uv1) has 112
+ to access the fat SGI UV2000 SMP machine. The machine (uv1) has 112
Intel IvyBridge cores at 3.3GHz and 3.25TB RAM. An PI> *needs
explicitly* ask
[support](https://support.it4i.cz/rt/) for
@@ -185,13 +193,13 @@ is allowed after request for this queue.
after exhaustion of computational resources.). It is required that
active project is specified to enter the queue, however no remaining
resources are required. Consumed resources will be accounted to
- the Project. Only 178 nodes without accelerator may be ed from
+ the Project. Only 178 nodes without accelerator may be accessed from
this queue. Full nodes, 24 cores per node are allocated. The queue
runs with very low priority and no special authorization is required
to use it. The maximum runtime in qfree is 12 hours.
- **qviz**, the Visualization queue****: Intended for
pre-/post-processing using OpenGL accelerated graphics. Currently
- when ing the node, each user gets 4 cores of a CPU allocated,
+ when accessing the node, each user gets 4 cores of a CPU allocated,
thus approximately 73 GB of RAM and 1/7 of the GPU capacity
(default "chunk"). *If more GPU power or RAM is required, it is
recommended to allocate more chunks (with 4 cores each) up to one
@@ -202,7 +210,7 @@ is allowed after request for this queue.
-To node with Xeon Phi co-processor user needs to specify that in
+To access node with Xeon Phi co-processor user needs to specify that in
[job submission select
statement](job-submission-and-execution.html).
@@ -228,7 +236,7 @@ Check the status of jobs, queues and compute nodes at
-
+
@@ -335,3 +343,5 @@ Password:
+
+
diff --git a/converted/docs.it4i.cz/salomon/software/ansys/ansys-cfx.md b/converted/docs.it4i.cz/salomon/software/ansys/ansys-cfx.md
index e6d4672e..7710a024 100644
--- a/converted/docs.it4i.cz/salomon/software/ansys/ansys-cfx.md
+++ b/converted/docs.it4i.cz/salomon/software/ansys/ansys-cfx.md
@@ -1,6 +1,14 @@
ANSYS CFX
=========
+
+
+
+
+
+
+
+
[ANSYS
CFX](http://www.ansys.com/Products/Simulation+Technology/Fluid+Dynamics/Fluid+Dynamics+Products/ANSYS+CFX)
software is a high-performance, general purpose fluid dynamics program
@@ -48,7 +56,7 @@ cfx.pbs script and execute it via the qsub command.
do
if [ "$hl" = "" ]
then hl="$host:$procs_per_host"
- else hl="$:$host:$procs_per_host"
+ else hl="${hl}:$host:$procs_per_host"
fi
done
@@ -87,3 +95,4 @@ preferences](setting-license-preferences.html) instead.
+
diff --git a/converted/docs.it4i.cz/salomon/software/ansys/ansys-fluent.md b/converted/docs.it4i.cz/salomon/software/ansys/ansys-fluent.md
index 8006674a..7c1cb2e4 100644
--- a/converted/docs.it4i.cz/salomon/software/ansys/ansys-fluent.md
+++ b/converted/docs.it4i.cz/salomon/software/ansys/ansys-fluent.md
@@ -1,6 +1,14 @@
ANSYS Fluent
============
+
+
+
+
+
+
+
+
[ANSYS
Fluent](http://www.ansys.com/Products/Simulation+Technology/Fluid+Dynamics/Fluid+Dynamics+Products/ANSYS+Fluent)
software contains the broad physical modeling capabilities needed to
@@ -144,6 +152,14 @@ execute the job across multiple processors.
+
+
+
+
+
+
+
+
>To run ANSYS Fluent in batch mode with user's config file you can
utilize/modify the following script and execute it via the qsub
command.
@@ -176,7 +192,7 @@ command.
cpus=‘expr $num_nodes * $NCPUS‘
#Default arguments for mpp jobs, these should be changed to suit your
#needs.
- fluent_args="-t$ $fluent_args -cnf=$PBS_NODEFILE"
+ fluent_args="-t${cpus} $fluent_args -cnf=$PBS_NODEFILE"
;;
*)
#SMP case
@@ -215,3 +231,5 @@ run](setting-license-preferences.html).
+
+
diff --git a/converted/docs.it4i.cz/salomon/software/ansys/ansys-ls-dyna.md b/converted/docs.it4i.cz/salomon/software/ansys/ansys-ls-dyna.md
index 9ff80553..a1189274 100644
--- a/converted/docs.it4i.cz/salomon/software/ansys/ansys-ls-dyna.md
+++ b/converted/docs.it4i.cz/salomon/software/ansys/ansys-ls-dyna.md
@@ -1,9 +1,17 @@
ANSYS LS-DYNA
=============
+
+
+
+
+
+
+
+
[ANSYS
LS-DYNA](http://www.ansys.com/Products/Simulation+Technology/Structural+Mechanics/Explicit+Dynamics/ANSYS+LS-DYNA)
-software provides convenient and easy-to-use to the
+software provides convenient and easy-to-use access to the
technology-rich, time-tested explicit solver without the need to contend
with the complex input requirements of this sophisticated program.
Introduced in 1996, ANSYS LS-DYNA capabilities have helped customers in
@@ -52,7 +60,7 @@ default ansysdyna.pbs script and execute it via the qsub command.
do
if [ "$hl" = "" ]
then hl="$host:$procs_per_host"
- else hl="$:$host:$procs_per_host"
+ else hl="${hl}:$host:$procs_per_host"
fi
done
@@ -87,3 +95,4 @@ will fail.
+
diff --git a/converted/docs.it4i.cz/salomon/software/ansys/ansys-mechanical-apdl.md b/converted/docs.it4i.cz/salomon/software/ansys/ansys-mechanical-apdl.md
index 7aac5b95..0c3c6d9b 100644
--- a/converted/docs.it4i.cz/salomon/software/ansys/ansys-mechanical-apdl.md
+++ b/converted/docs.it4i.cz/salomon/software/ansys/ansys-mechanical-apdl.md
@@ -1,6 +1,14 @@
ANSYS MAPDL
===========
+
+
+
+
+
+
+
+
>**[ANSYS
Multiphysics](http://www.ansys.com/Products/Simulation+Technology/Structural+Mechanics/ANSYS+Multiphysics)**
software offers a comprehensive product solution for both multiphysics
@@ -43,7 +51,7 @@ default mapdl.pbs script and execute it via the qsub command.
do
if [ "$hl" = "" ]
then hl="$host:$procs_per_host"
- else hl="$:$host:$procs_per_host"
+ else hl="${hl}:$host:$procs_per_host"
fi
done
@@ -80,3 +88,4 @@ AUTODYN)>
+
diff --git a/converted/docs.it4i.cz/salomon/software/ansys/ansys-products-mechanical-fluent-cfx-mapdl.md b/converted/docs.it4i.cz/salomon/software/ansys/ansys-products-mechanical-fluent-cfx-mapdl.md
index 4e3c1f73..97420ddb 100644
--- a/converted/docs.it4i.cz/salomon/software/ansys/ansys-products-mechanical-fluent-cfx-mapdl.md
+++ b/converted/docs.it4i.cz/salomon/software/ansys/ansys-products-mechanical-fluent-cfx-mapdl.md
@@ -1,6 +1,14 @@
Overview of ANSYS Products
==========================
+
+
+
+
+
+
+
+
[SVS FEM](http://www.svsfem.cz/)** as ***[ANSYS
Channel partner](http://www.ansys.com/)*** for Czech
Republic provided all ANSYS licenses for all clusters and supports of
@@ -31,3 +39,4 @@ solution to the clusters directly from the client's Workbench project
+
diff --git a/converted/docs.it4i.cz/salomon/software/ansys/ansys.md b/converted/docs.it4i.cz/salomon/software/ansys/ansys.md
index 6101ad91..82ff875b 100644
--- a/converted/docs.it4i.cz/salomon/software/ansys/ansys.md
+++ b/converted/docs.it4i.cz/salomon/software/ansys/ansys.md
@@ -1,6 +1,14 @@
Overview of ANSYS Products
==========================
+
+
+
+
+
+
+
+
[SVS FEM](http://www.svsfem.cz/)** as ***[ANSYS
Channel partner](http://www.ansys.com/)*** for Czech
Republic provided all ANSYS licenses for all clusters and supports of
diff --git a/converted/docs.it4i.cz/salomon/software/ansys/licensing.md b/converted/docs.it4i.cz/salomon/software/ansys/licensing.md
index 5d09c5ae..55a0acbe 100644
--- a/converted/docs.it4i.cz/salomon/software/ansys/licensing.md
+++ b/converted/docs.it4i.cz/salomon/software/ansys/licensing.md
@@ -1,6 +1,14 @@
Licensing and Available Versions
================================
+
+
+
+
+
+
+
+
ANSYS licence can be used by:
-----------------------------
@@ -42,3 +50,7 @@ Please [see this page to set license
preferences](setting-license-preferences.html).
+
+
+
+
diff --git a/converted/docs.it4i.cz/salomon/software/ansys/setting-license-preferences.md b/converted/docs.it4i.cz/salomon/software/ansys/setting-license-preferences.md
index b3c44f8f..e12e3b69 100644
--- a/converted/docs.it4i.cz/salomon/software/ansys/setting-license-preferences.md
+++ b/converted/docs.it4i.cz/salomon/software/ansys/setting-license-preferences.md
@@ -1,6 +1,14 @@
Setting license preferences
===========================
+
+
+
+
+
+
+
+
Some ANSYS tools allow you to explicitly specify usage of academic or
commercial licenses in the command line (eg.
ansys161 -p aa_r to select Academic Research
@@ -17,11 +25,11 @@ Launch the ANSLIC_ADMIN utility in a graphical environment:
ANSLIC_ADMIN Utility will be run
-
+
-
+
-
+
@@ -30,7 +38,8 @@ the bottom of the list.
-
+
+
diff --git a/converted/docs.it4i.cz/salomon/software/ansys/workbench.md b/converted/docs.it4i.cz/salomon/software/ansys/workbench.md
index 11091bd1..34ce793b 100644
--- a/converted/docs.it4i.cz/salomon/software/ansys/workbench.md
+++ b/converted/docs.it4i.cz/salomon/software/ansys/workbench.md
@@ -1,6 +1,14 @@
Workbench
=========
+
+
+
+
+
+
+
+
Workbench Batch Mode
--------------------
@@ -74,3 +82,4 @@ uploading a project from your local computer.
+
diff --git a/converted/docs.it4i.cz/salomon/software/chemistry/molpro.md b/converted/docs.it4i.cz/salomon/software/chemistry/molpro.md
index 77cf1643..80e64cdb 100644
--- a/converted/docs.it4i.cz/salomon/software/chemistry/molpro.md
+++ b/converted/docs.it4i.cz/salomon/software/chemistry/molpro.md
@@ -1,8 +1,20 @@
Molpro
======
+
+
+
+
Molpro is a complete system of ab initio programs for molecular
electronic structure calculations.
+
+
+
+
+
+
+
+
About Molpro
------------
@@ -14,7 +26,7 @@ License
-------
Molpro software package is available only to users that have a valid
-license. Please contact support to enable to Molpro if you have a
+license. Please contact support to enable access to Molpro if you have a
valid license appropriate for running on our cluster (eg. >academic
research group licence, parallel execution).
diff --git a/converted/docs.it4i.cz/salomon/software/chemistry/nwchem.md b/converted/docs.it4i.cz/salomon/software/chemistry/nwchem.md
index 18d279ce..cda2a674 100644
--- a/converted/docs.it4i.cz/salomon/software/chemistry/nwchem.md
+++ b/converted/docs.it4i.cz/salomon/software/chemistry/nwchem.md
@@ -1,7 +1,19 @@
NWChem
======
+
+
+
+
High-Performance Computational Chemistry
+
+
+
+
+
+
+
+
>Introduction
-------------------------
diff --git a/converted/docs.it4i.cz/salomon/software/chemistry/phono3py.md b/converted/docs.it4i.cz/salomon/software/chemistry/phono3py.md
index 4aeb4257..a508b612 100644
--- a/converted/docs.it4i.cz/salomon/software/chemistry/phono3py.md
+++ b/converted/docs.it4i.cz/salomon/software/chemistry/phono3py.md
@@ -4,6 +4,18 @@ Phono3py
+
+
+
+
+
+
+
+
+
+
+
+
Introduction
-------------
@@ -203,3 +215,7 @@ grouping single conductivity per grid calculations using
```
$ phono3py --fc3 --fc2 --dim="2 2 2" --mesh="9 9 9" --br --read_gamma
```
+
+
+
+
diff --git a/converted/docs.it4i.cz/salomon/software/compilers.md b/converted/docs.it4i.cz/salomon/software/compilers.md
index 5dca15f3..0967a0ff 100644
--- a/converted/docs.it4i.cz/salomon/software/compilers.md
+++ b/converted/docs.it4i.cz/salomon/software/compilers.md
@@ -1,11 +1,23 @@
Compilers
=========
+
+
+
+
Available compilers, including GNU, INTEL and UPC compilers
+
+
+
+
+
+
+
+
There are several compilers for different programming languages
available on the cluster:
@@ -63,7 +75,7 @@ GNU
For compatibility reasons there are still available the original (old
4.4.7-11) versions of GNU compilers as part of the OS. These are
-ible in the search path by default.
+accessible in the search path by default.
It is strongly recommended to use the up to date version which comes
with the module GCC:
diff --git a/converted/docs.it4i.cz/salomon/software/comsol/comsol-multiphysics.md b/converted/docs.it4i.cz/salomon/software/comsol/comsol-multiphysics.md
index a4446f41..a2f4edd3 100644
--- a/converted/docs.it4i.cz/salomon/software/comsol/comsol-multiphysics.md
+++ b/converted/docs.it4i.cz/salomon/software/comsol/comsol-multiphysics.md
@@ -5,11 +5,19 @@ COMSOL Multiphysics®
+
+
+
+
+
+
+
+
>>Introduction
-------------------------
->>[COMSOL](http://www.comsol.com)><span>
+>>[COMSOL](http://www.comsol.com)
is a powerful environment for modelling and solving various engineering
and scientific problems based on partial differential equations. COMSOL
is designed to solve coupled or multiphysics phenomena. For many
@@ -37,7 +45,7 @@ applications.
others](http://www.comsol.com/products)
>>COMSOL also allows an
->>><span>interface support for
+>>interface support for
equation-based modelling of
>>partial differential
equations.
@@ -49,18 +57,18 @@ equations.
>>On the clusters COMSOL is available in the latest stable
version. There are two variants of the release:
-- >>**Non commercial**><span> or so
+- >>**Non commercial** or so
called >>**EDU
variant**>>, which can be used for research
and educational purposes.
-- >>**Commercial**><span> or so called
- >>**COM variant**><span>,
+- >>**Commercial** or so called
+ >>**COM variant**,
which can used also for commercial activities.
- >>**COM variant**><span>
+ >>**COM variant**
has only subset of features compared to the
>>**EDU
- variant**>> available.
+ variant**>> available. <span
id="result_box"
More about
licensing will be posted here
@@ -73,7 +81,7 @@ version. There are two variants of the release:
$ module load COMSOL/51-EDU
```
->>By default the ><span>**EDU
+>>By default the **EDU
variant**>> will be loaded. If user needs other
version or variant, load the particular version. To obtain the list of
available versions use
@@ -86,7 +94,7 @@ $ module avail COMSOL
it is recommend to use COMSOL on the compute nodes via PBS Pro
scheduler. In order run the COMSOL Desktop GUI on Windows is recommended
to use the [Virtual Network Computing
-(VNC)](../../../get-started-with-it4innovations/ing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html).
+(VNC)](../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html).
```
$ xhost +
@@ -121,7 +129,7 @@ module load COMSOL
ntask=$(wc -l $PBS_NODEFILE)
-comsol -nn $ batch -configuration /tmp –mpiarg –rmk –mpiarg pbs -tmpdir /scratch/$USER/ -inputfile name_input_f.mph -outputfile name_output_f.mph -batchlog name_log_f.log
+comsol -nn ${ntask} batch -configuration /tmp –mpiarg –rmk –mpiarg pbs -tmpdir /scratch/$USER/ -inputfile name_input_f.mph -outputfile name_output_f.mph -batchlog name_log_f.log
```
>>Working directory has to be created before sending the
@@ -130,25 +138,25 @@ has to be in working directory or full path to input file has to be
specified. The appropriate path to the temp directory of the job has to
be set by command option (-tmpdir).
-LiveLink™* *for MATLAB^®^
+LiveLink™* *for MATLAB®^
-------------------------
>>COMSOL is the software package for the numerical solution of
the partial differential equations. LiveLink for MATLAB allows
connection to the
-COMSOL>>^><span><span><span><span>**®**</span></span></span></span></span>^
+COMSOL>><span><span><span><span><span>**®**</span></span></span></span></span>^
API (Application Programming Interface) with the benefits of the
programming language and computing environment of the MATLAB.
>>LiveLink for MATLAB is available in both
->>**EDU**><span> and
->>**COM**><span>
->>**variant**><span> of the
+>>**EDU** and
+>>**COM**
+>>**variant** of the
COMSOL release. On the clusters 1 commercial
-(>>**COM**><span>) license
+(>>**COM**) license
and the 5 educational
-(>>**EDU**><span>) licenses
+(>>**EDU**) licenses
of LiveLink for MATLAB (please see the [ISV
Licenses](../isv_licenses.html)) are available.
Following example shows how to start COMSOL model from MATLAB via
@@ -192,7 +200,7 @@ module load COMSOL/51-EDU
ntask=$(wc -l $PBS_NODEFILE)
-comsol -nn $ server -configuration /tmp -mpiarg -rmk -mpiarg pbs -tmpdir /scratch/work/user/$USER/work &
+comsol -nn ${ntask} server -configuration /tmp -mpiarg -rmk -mpiarg pbs -tmpdir /scratch/work/user/$USER/work &
cd /apps/cae/COMSOL/51/mli
matlab -nodesktop -nosplash -r "mphstart; addpath /scratch/work/user/$USER/work; test_job"
```
@@ -206,3 +214,6 @@ path to input file has to be specified. The Matlab command option (-r
port number.
+
+
+
diff --git a/converted/docs.it4i.cz/salomon/software/comsol/licensing-and-available-versions.md b/converted/docs.it4i.cz/salomon/software/comsol/licensing-and-available-versions.md
index 4cd91829..22be0cc0 100644
--- a/converted/docs.it4i.cz/salomon/software/comsol/licensing-and-available-versions.md
+++ b/converted/docs.it4i.cz/salomon/software/comsol/licensing-and-available-versions.md
@@ -1,6 +1,14 @@
Licensing and Available Versions
================================
+
+
+
+
+
+
+
+
Comsol licence can be used by:
------------------------------
@@ -27,7 +35,7 @@ Comsol COM Network Licence
The licence intended to be used for science and research, publications,
students’ projects, commercial research with no commercial use
-restrictions. id="result_box"> E
+restrictions. id="result_box"> E<span
nables the solution
of at least one job
by one user in one
@@ -37,3 +45,7 @@ Available Versions
------------------
- ver. 51
+
+
+
+
diff --git a/converted/docs.it4i.cz/salomon/software/debuggers.md b/converted/docs.it4i.cz/salomon/software/debuggers.md
index 49d0dfc9..b2430cc6 100644
--- a/converted/docs.it4i.cz/salomon/software/debuggers.md
+++ b/converted/docs.it4i.cz/salomon/software/debuggers.md
@@ -5,6 +5,14 @@ Debuggers and profilers summary
+
+
+
+
+
+
+
+
Introduction
------------
@@ -22,7 +30,7 @@ The intel debugger version 13.0 is available, via module intel. The
debugger works for applications compiled with C and C++ compiler and the
ifort fortran 77/90/95 compiler. The debugger provides java GUI
environment. Use [X
-display](../../get-started-with-it4innovations/ing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html)
+display](../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html)
for running the GUI.
$ module load intel
diff --git a/converted/docs.it4i.cz/salomon/software/debuggers/aislinn.md b/converted/docs.it4i.cz/salomon/software/debuggers/aislinn.md
index 451b73a0..339c5ebb 100644
--- a/converted/docs.it4i.cz/salomon/software/debuggers/aislinn.md
+++ b/converted/docs.it4i.cz/salomon/software/debuggers/aislinn.md
@@ -1,11 +1,19 @@
Aislinn
=======
+
+
+
+
+
+
+
+
- Aislinn is a dynamic verifier for MPI programs. For a fixed input it
covers all possible runs with respect to nondeterminism introduced
by MPI. It allows to detect bugs (for sure) that occurs very rare in
normal runs.
-- Aislinn detects problems like invalid memory es, deadlocks,
+- Aislinn detects problems like invalid memory accesses, deadlocks,
misuse of MPI, and resource leaks.
- Aislinn is open-source software; you can use it without any
licensing limitations.
@@ -17,6 +25,10 @@ Note
Aislinn is software developed at IT4Innovations and some parts are still
considered experimental. If you have any questions or experienced any
problems, please contact the author: <stanislav.bohm@vsb.cz>.
+
+
+
+
### Usage
Let us have the following program that contains a bug that is not
@@ -112,6 +124,10 @@ It shows us:
> - The last part shows MPI calls for each process that occurs in the
> invalid run. The more detailed information about each call can be
> obtained by mouse cursor.
+
+
+
+
### Limitations
Since the verification is a non-trivial process there are some of
@@ -148,3 +164,7 @@ will be removed in the future:
reads inputs and writes results, it is ok.
+
+
+
+
diff --git a/converted/docs.it4i.cz/salomon/software/debuggers/allinea-ddt.md b/converted/docs.it4i.cz/salomon/software/debuggers/allinea-ddt.md
index 4e1b2df7..64b4024a 100644
--- a/converted/docs.it4i.cz/salomon/software/debuggers/allinea-ddt.md
+++ b/converted/docs.it4i.cz/salomon/software/debuggers/allinea-ddt.md
@@ -5,6 +5,14 @@ Allinea Forge (DDT,MAP)
+
+
+
+
+
+
+
+
Allinea Forge consist of two tools - debugger DDT and profiler MAP.
Allinea DDT, is a commercial debugger primarily for debugging parallel
@@ -59,11 +67,11 @@ $ mpif90 -g -O0 -o test_debug test.f
Before debugging, you need to compile your code with theses flags:
--g** : Generates extra debugging information usable by GDB. -g3
+-g** : Generates extra debugging information usable by GDB. -g3**
includes even more debugging information. This option is available for
GNU and INTEL C/C++ and Fortran compilers.
--O0** : Suppress all optimizations.
+-O0** : Suppress all optimizations.**
@@ -72,15 +80,15 @@ Direct starting a Job with Forge
Be sure to log in with an [ X window
forwarding
-enabled](../../../get-started-with-it4innovations/ing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html).
+enabled](../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html).
This could mean using the -X in the ssh:
$ ssh -X username@clustername.it4i.cz
-Other options is to login node using VNC. Please see the detailed
+Other options is to access login node using VNC. Please see the detailed
information on [how to
use graphic user interface on the
-clusters](../../../get-started-with-it4innovations/ing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html)
+clusters](../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html)
.
From the login node an interactive session **with X windows forwarding**
@@ -106,7 +114,7 @@ Command line arguments to a program can be entered to the
box.
-
+
To start the debugging directly without the submission window, user can
specify the debugging and execution parameters from the command line.
@@ -154,7 +162,7 @@ It is recommended to set the following environment values on the offload
host:
export MYO_WATCHDOG_MONITOR=-1 # To make sure the host process isn't killed when we enter a debugging session
- export AMPLXE_COI_DEBUG_SUPPORT=true # To make sure that debugging symbols are ible on the host and the card
+ export AMPLXE_COI_DEBUG_SUPPORT=true # To make sure that debugging symbols are accessible on the host and the card
unset OFFLOAD_MAIN # To make sure allinea DDT can attach to offloaded codes
Then use one of the above mentioned methods to launch Forge. (Reverse
@@ -223,3 +231,5 @@ Debugging with Allinea DDT, Workshop conducted at LLNL by Allinea on May
+
+
diff --git a/converted/docs.it4i.cz/salomon/software/debuggers/allinea-performance-reports.md b/converted/docs.it4i.cz/salomon/software/debuggers/allinea-performance-reports.md
index 390af289..e1fffc40 100644
--- a/converted/docs.it4i.cz/salomon/software/debuggers/allinea-performance-reports.md
+++ b/converted/docs.it4i.cz/salomon/software/debuggers/allinea-performance-reports.md
@@ -1,11 +1,23 @@
Allinea Performance Reports
===========================
+
+
+
+
quick application profiling
+
+
+
+
+
+
+
+
Introduction
------------
@@ -75,3 +87,6 @@ and
were created. We can see that the code is very efficient on MPI and is
CPU bounded.
+
+
+
diff --git a/converted/docs.it4i.cz/salomon/software/debuggers/intel-vtune-amplifier.md b/converted/docs.it4i.cz/salomon/software/debuggers/intel-vtune-amplifier.md
index 51dbe438..6a82738a 100644
--- a/converted/docs.it4i.cz/salomon/software/debuggers/intel-vtune-amplifier.md
+++ b/converted/docs.it4i.cz/salomon/software/debuggers/intel-vtune-amplifier.md
@@ -5,6 +5,14 @@ Intel VTune Amplifier XE
+
+
+
+
+
+
+
+
Introduction
------------
@@ -19,7 +27,11 @@ highlight of the features:
bandwidth
- Power usage analysis - frequency and sleep states.
-
+
+
+
+
+
@@ -139,3 +151,6 @@ References
3.>><https://software.intel.com/en-us/amplifier_help_linux> Linux
user guide
+
+
+
diff --git a/converted/docs.it4i.cz/salomon/software/debuggers/report.png b/converted/docs.it4i.cz/salomon/software/debuggers/report.png
new file mode 100644
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diff --git a/converted/docs.it4i.cz/salomon/software/debuggers/summary.md b/converted/docs.it4i.cz/salomon/software/debuggers/summary.md
index d649fa53..b1fe9677 100644
--- a/converted/docs.it4i.cz/salomon/software/debuggers/summary.md
+++ b/converted/docs.it4i.cz/salomon/software/debuggers/summary.md
@@ -5,6 +5,14 @@ Debuggers and profilers summary
+
+
+
+
+
+
+
+
Introduction
------------
@@ -22,7 +30,7 @@ The intel debugger version 13.0 is available, via module intel. The
debugger works for applications compiled with C and C++ compiler and the
ifort fortran 77/90/95 compiler. The debugger provides java GUI
environment. Use [X
-display](../../../get-started-with-it4innovations/ing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html)
+display](../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html)
for running the GUI.
$ module load intel
diff --git a/converted/docs.it4i.cz/salomon/software/debuggers/total-view.md b/converted/docs.it4i.cz/salomon/software/debuggers/total-view.md
index db26eae9..9159d2e9 100644
--- a/converted/docs.it4i.cz/salomon/software/debuggers/total-view.md
+++ b/converted/docs.it4i.cz/salomon/software/debuggers/total-view.md
@@ -1,8 +1,20 @@
Total View
==========
+
+
+
+
TotalView is a GUI-based source code multi-process, multi-thread
debugger.
+
+
+
+
+
+
+
+
License and Limitations for cluster Users
-----------------------------------------
@@ -42,11 +54,11 @@ Compile the code:
Before debugging, you need to compile your code with theses flags:
--g** : Generates extra debugging information usable by GDB. -g3
+-g** : Generates extra debugging information usable by GDB. -g3**
includes even more debugging information. This option is available for
GNU and INTEL C/C++ and Fortran compilers.
--O0** : Suppress all optimizations.
+-O0** : Suppress all optimizations.**
Starting a Job with TotalView
-----------------------------
@@ -56,7 +68,7 @@ using the -X in the ssh:
ssh -X username@salomon.it4i.cz
-Other options is to login node using VNC. Please see the detailed
+Other options is to access login node using VNC. Please see the detailed
information on how to use graphic user interface on Anselm
[here](https://docs.it4i.cz/salomon/software/debuggers/resolveuid/11e53ad0d2fd4c5187537f4baeedff33#VNC).
@@ -83,8 +95,8 @@ Please note:** To be able to run parallel debugging procedure from the
command line without stopping the debugger in the mpiexec source code
you have to add the following function to your **~/.tvdrc** file:
- proc mpi_auto_run_starter {
- set starter_programs
+ proc mpi_auto_run_starter {loaded_id} {
+ set starter_programs {mpirun mpiexec orterun}
set executable_name [TV::symbol get $loaded_id full_pathname]
set file_component [file tail $executable_name]
@@ -124,7 +136,7 @@ When following dialog appears click on "Yes"
At this point the main TotalView GUI window will appear and you can
insert the breakpoints and start debugging:
-
+
### Debugging a parallel code - option 2
@@ -154,3 +166,6 @@ documentation](http://www.roguewave.com/support/product-documentation/totalview-
web page is a good resource for learning more about some of the advanced
TotalView features.
+
+
+
diff --git a/converted/docs.it4i.cz/salomon/software/debuggers/valgrind.md b/converted/docs.it4i.cz/salomon/software/debuggers/valgrind.md
index 27c51bce..de33465d 100644
--- a/converted/docs.it4i.cz/salomon/software/debuggers/valgrind.md
+++ b/converted/docs.it4i.cz/salomon/software/debuggers/valgrind.md
@@ -1,7 +1,19 @@
Valgrind
========
+
+
+
+
Valgrind is a tool for memory debugging and profiling.
+
+
+
+
+
+
+
+
About Valgrind
--------------
@@ -20,8 +32,8 @@ Valgrind run 5-100 times slower.
The main tools available in Valgrind are :
- **Memcheck**, the original, must used and default tool. Verifies
- memory in you program and can detect use of unitialized
- memory, out of bounds memory , memory leaks, double free, etc.
+ memory access in you program and can detect use of unitialized
+ memory, out of bounds memory access, memory leaks, double free, etc.
- **Massif**, a heap profiler.
- **Hellgrind** and **DRD** can detect race conditions in
multi-threaded applications.
@@ -121,7 +133,7 @@ description of command line options.
==12652== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 6 from 6)
In the output we can see that Valgrind has detected both errors - the
-off-by-one memory at line 5 and a memory leak of 40 bytes. If we
+off-by-one memory access at line 5 and a memory leak of 40 bytes. If we
want a detailed analysis of the memory leak, we need to run Valgrind
with --leak-check=full option :
diff --git a/converted/docs.it4i.cz/salomon/software/debuggers/vampir.md b/converted/docs.it4i.cz/salomon/software/debuggers/vampir.md
index 4fb7ad88..a0b44fbd 100644
--- a/converted/docs.it4i.cz/salomon/software/debuggers/vampir.md
+++ b/converted/docs.it4i.cz/salomon/software/debuggers/vampir.md
@@ -1,13 +1,21 @@
Vampir
======
+
+
+
+
+
+
+
+
Vampir is a commercial trace analysis and visualisation tool. It can
work with traces in OTF and OTF2 formats. It does not have the
functionality to collect traces, you need to use a trace collection tool
(such as [Score-P](score-p.html)) first to collect the
traces.
-
+
----------------------------------------------------------------------------------------------------------------------------------------------
Installed versions
diff --git a/converted/docs.it4i.cz/salomon/software/intel-suite/intel-advisor.md b/converted/docs.it4i.cz/salomon/software/intel-suite/intel-advisor.md
index 12a07b71..a2c1b218 100644
--- a/converted/docs.it4i.cz/salomon/software/intel-suite/intel-advisor.md
+++ b/converted/docs.it4i.cz/salomon/software/intel-suite/intel-advisor.md
@@ -1,6 +1,14 @@
Intel Advisor
=============
+
+
+
+
+
+
+
+
is tool aiming to assist you in vectorization and threading of your
code. You can use it to profile your application and identify
loops, that could benefit from vectorization and/or threading
diff --git a/converted/docs.it4i.cz/salomon/software/intel-suite/intel-compilers.md b/converted/docs.it4i.cz/salomon/software/intel-suite/intel-compilers.md
index 6dd1fa07..5d8661a9 100644
--- a/converted/docs.it4i.cz/salomon/software/intel-suite/intel-compilers.md
+++ b/converted/docs.it4i.cz/salomon/software/intel-suite/intel-compilers.md
@@ -5,6 +5,14 @@ Intel Compilers
+
+
+
+
+
+
+
+
The Intel compilers in multiple versions are available, via module
intel. The compilers include the icc C and C++ compiler and the ifort
fortran 77/90/95 compiler.
diff --git a/converted/docs.it4i.cz/salomon/software/intel-suite/intel-debugger.md b/converted/docs.it4i.cz/salomon/software/intel-suite/intel-debugger.md
index 82f38d17..b1663cee 100644
--- a/converted/docs.it4i.cz/salomon/software/intel-suite/intel-debugger.md
+++ b/converted/docs.it4i.cz/salomon/software/intel-suite/intel-debugger.md
@@ -5,6 +5,14 @@ Intel Debugger
+
+
+
+
+
+
+
+
IDB is no longer available since Intel Parallel Studio 2015
Debugging serial applications
@@ -14,7 +22,7 @@ The intel debugger version 13.0 is available, via module intel. The
debugger works for applications compiled with C and C++ compiler and the
ifort fortran 77/90/95 compiler. The debugger provides java GUI
environment. Use [X
-display](../../../get-started-with-it4innovations/ing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html)
+display](../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html)
for running the GUI.
$ module load intel/2014.06
@@ -26,9 +34,9 @@ The debugger may run in text mode. To debug in text mode, use
$ idbc
To debug on the compute nodes, module intel must be loaded.
-The GUI on compute nodes may be ed using the same way as in [the
+The GUI on compute nodes may be accessed using the same way as in [the
GUI
-section](../../../get-started-with-it4innovations/ing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html)
+section](../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html)
Example:
@@ -43,7 +51,7 @@ Example:
In this example, we allocate 1 full compute node, compile program
myprog.c with debugging options -O0 -g and run the idb debugger
-interactively on the myprog.x executable. The GUI is via X11 port
+interactively on the myprog.x executable. The GUI access is via X11 port
forwarding provided by the PBS workload manager.
Debugging parallel applications
@@ -56,7 +64,7 @@ programs as well.
For debugging small number of MPI ranks, you may execute and debug each
rank in separate xterm terminal (do not forget the [X
-display](../../../get-started-with-it4innovations/ing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html)).
+display](../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html)).
Using Intel MPI, this may be done in following way:
$ qsub -q qexp -l select=2:ncpus=24 -X -I
diff --git a/converted/docs.it4i.cz/salomon/software/intel-suite/intel-inspector.md b/converted/docs.it4i.cz/salomon/software/intel-suite/intel-inspector.md
index dce70676..17209fd2 100644
--- a/converted/docs.it4i.cz/salomon/software/intel-suite/intel-inspector.md
+++ b/converted/docs.it4i.cz/salomon/software/intel-suite/intel-inspector.md
@@ -1,6 +1,14 @@
Intel Inspector
===============
+
+
+
+
+
+
+
+
Intel Inspector is a dynamic memory and threading error checking tool
for C/C++/Fortran applications. It can detect issues such as memory
leaks, invalid memory references, uninitalized variables, race
diff --git a/converted/docs.it4i.cz/salomon/software/intel-suite/intel-integrated-performance-primitives.md b/converted/docs.it4i.cz/salomon/software/intel-suite/intel-integrated-performance-primitives.md
index e0b1bf13..d62f7400 100644
--- a/converted/docs.it4i.cz/salomon/software/intel-suite/intel-integrated-performance-primitives.md
+++ b/converted/docs.it4i.cz/salomon/software/intel-suite/intel-integrated-performance-primitives.md
@@ -5,6 +5,14 @@ Intel IPP
+
+
+
+
+
+
+
+
Intel Integrated Performance Primitives
---------------------------------------
diff --git a/converted/docs.it4i.cz/salomon/software/intel-suite/intel-mkl.md b/converted/docs.it4i.cz/salomon/software/intel-suite/intel-mkl.md
index 43cb59ba..23e0781b 100644
--- a/converted/docs.it4i.cz/salomon/software/intel-suite/intel-mkl.md
+++ b/converted/docs.it4i.cz/salomon/software/intel-suite/intel-mkl.md
@@ -6,6 +6,14 @@ Intel MKL
+
+
+
+
+
+
+
+
Intel Math Kernel Library
-------------------------
@@ -88,7 +96,7 @@ With intel compiler use -mkl option to link default threaded MKL.
Intel MKL library provides number of interfaces. The fundamental once
are the LP64 and ILP64. The Intel MKL ILP64 libraries use the 64-bit
integer type (necessary for indexing large arrays, with more than
-2^31^-1 elements), whereas the LP64 libraries index arrays with the
+231^-1 elements), whereas the LP64 libraries index arrays with the
32-bit integer type.
Interface Integer type
diff --git a/converted/docs.it4i.cz/salomon/software/intel-suite/intel-parallel-studio-introduction.md b/converted/docs.it4i.cz/salomon/software/intel-suite/intel-parallel-studio-introduction.md
index 498b7c9d..3a8c44f5 100644
--- a/converted/docs.it4i.cz/salomon/software/intel-suite/intel-parallel-studio-introduction.md
+++ b/converted/docs.it4i.cz/salomon/software/intel-suite/intel-parallel-studio-introduction.md
@@ -5,6 +5,14 @@ Intel Parallel Studio
+
+
+
+
+
+
+
+
The Salomon cluster provides following elements of the Intel Parallel
Studio XE
@@ -42,7 +50,7 @@ IDB is no longer available since Parallel Studio 2015.
debugger works for applications compiled with C and C++ compiler and the
ifort fortran 77/90/95 compiler. The debugger provides java GUI
environment. Use [X
-display](../../../get-started-with-it4innovations/ing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html)
+display](../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html)
for running the GUI.
$ module load intel
diff --git a/converted/docs.it4i.cz/salomon/software/intel-suite/intel-tbb.md b/converted/docs.it4i.cz/salomon/software/intel-suite/intel-tbb.md
index bdc4e31e..84d45ce7 100644
--- a/converted/docs.it4i.cz/salomon/software/intel-suite/intel-tbb.md
+++ b/converted/docs.it4i.cz/salomon/software/intel-suite/intel-tbb.md
@@ -5,6 +5,14 @@ Intel TBB
+
+
+
+
+
+
+
+
Intel Threading Building Blocks
-------------------------------
diff --git a/converted/docs.it4i.cz/salomon/software/intel-suite/intel-trace-analyzer-and-collector.md b/converted/docs.it4i.cz/salomon/software/intel-suite/intel-trace-analyzer-and-collector.md
index 9f6cb95b..61dc40e4 100644
--- a/converted/docs.it4i.cz/salomon/software/intel-suite/intel-trace-analyzer-and-collector.md
+++ b/converted/docs.it4i.cz/salomon/software/intel-suite/intel-trace-analyzer-and-collector.md
@@ -1,6 +1,14 @@
Intel Trace Analyzer and Collector
==================================
+
+
+
+
+
+
+
+
Intel Trace Analyzer and Collector (ITAC) is a tool to collect and
graphicaly analyze behaviour of MPI applications. It helps you to
analyze communication patterns of your application, identify hotspots,
@@ -32,7 +40,7 @@ Viewing traces
--------------
To view and analyze the trace, open ITAC GUI in a [graphical
-environment](../../../get-started-with-it4innovations/ing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html)
+environment](../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html)
:
$ module load itac/9.1.2.024
diff --git a/converted/docs.it4i.cz/salomon/software/intel-xeon-phi.md b/converted/docs.it4i.cz/salomon/software/intel-xeon-phi.md
index c5684fdb..25b9b052 100644
--- a/converted/docs.it4i.cz/salomon/software/intel-xeon-phi.md
+++ b/converted/docs.it4i.cz/salomon/software/intel-xeon-phi.md
@@ -1,11 +1,23 @@
Intel Xeon Phi
==============
+
+
+
+
A guide to Intel Xeon Phi usage
+
+
+
+
+
+
+
+
Intel Xeon Phi accelerator can be programmed in several modes. The
default mode on the cluster is offload mode, but all modes described in
this document are supported.
@@ -13,7 +25,7 @@ this document are supported.
Intel Utilities for Xeon Phi
----------------------------
-To get to a compute node with Intel Xeon Phi accelerator, use the
+To get access to a compute node with Intel Xeon Phi accelerator, use the
PBS interactive session
$ qsub -I -q qprod -l select=1:ncpus=24:accelerator=True:naccelerators=2:accelerator_model=phi7120 -A NONE-0-0
@@ -510,7 +522,7 @@ Phi:
### Execution of the Program in Native Mode on Intel Xeon Phi
-The user to the Intel Xeon Phi is through the SSH. Since user
+The user access to the Intel Xeon Phi is through the SSH. Since user
home directories are mounted using NFS on the accelerator, users do not
have to copy binary files or libraries between the host and accelerator.
@@ -799,7 +811,7 @@ Similarly to execution of OpenMP programs in native mode, since the
environmental module are not supported on MIC, user has to setup paths
to Intel MPI libraries and binaries manually. One time setup can be done
by creating a "**.profile**" file in user's home directory. This file
-sets up the environment on the MIC automatically once user to the
+sets up the environment on the MIC automatically once user access to the
accelerator through the SSH.
At first get the LD_LIBRARY_PATH for currenty used Intel Compiler and
@@ -828,7 +840,7 @@ libraries.
library and particular version of an Intel compiler. These versions have
to match with loaded modules.
-To a MIC accelerator located on a node that user is currently
+To access a MIC accelerator located on a node that user is currently
connected to, use:
$ ssh mic0
@@ -898,7 +910,7 @@ execute:
Execution on host - MPI processes distributed over multiple
accelerators on multiple nodes**
->To get to multiple nodes with MIC accelerator, user has to
+>To get access to multiple nodes with MIC accelerator, user has to
use PBS to allocate the resources. To start interactive session, that
allocates 2 compute nodes = 2 MIC accelerators run qsub command with
following parameters:
@@ -919,7 +931,7 @@ immediately. To see the other nodes that have been allocated use:
r38u32n1001.bullx
>This output means that the PBS allocated nodes r38u31n1000 and
-r38u32n1001, which means that user has direct to
+r38u32n1001, which means that user has direct access to
"**r38u31n1000-mic0**" and "**>r38u32n1001-mic0**"
accelerators.
@@ -1067,11 +1079,11 @@ PBS also generates a set of node-files that can be used instead of
manually creating a new one every time. Three node-files are genereated:
Host only node-file:**
- - /lscratch/$/nodefile-cn
+ - /lscratch/${PBS_JOBID}/nodefile-cn
MIC only node-file**:
- - /lscratch/$/nodefile-mic
+ - /lscratch/${PBS_JOBID}/nodefile-mic
Host and MIC node-file**:
- - /lscratch/$/nodefile-mix
+ - /lscratch/${PBS_JOBID}/nodefile-mix
Please note each host or accelerator is listed only per files. User has
to specify how many jobs should be executed per node using "-n"
@@ -1084,3 +1096,7 @@ For more details about optimization techniques please read Intel
document [Optimization and Performance Tuning for Intel® Xeon Phi™
Coprocessors](http://software.intel.com/en-us/articles/optimization-and-performance-tuning-for-intel-xeon-phi-coprocessors-part-1-optimization "http://software.intel.com/en-us/articles/optimization-and-performance-tuning-for-intel-xeon-phi-coprocessors-part-1-optimization")
+
+
+
+
diff --git a/converted/docs.it4i.cz/salomon/software/java.md b/converted/docs.it4i.cz/salomon/software/java.md
index 2701936e..2ec6c2c8 100644
--- a/converted/docs.it4i.cz/salomon/software/java.md
+++ b/converted/docs.it4i.cz/salomon/software/java.md
@@ -1,11 +1,23 @@
Java
====
+
+
+
+
Java on the cluster
+
+
+
+
+
+
+
+
Java is available on the cluster. Activate java by loading the Java
module
diff --git a/converted/docs.it4i.cz/salomon/software/mpi-1/Running_OpenMPI.md b/converted/docs.it4i.cz/salomon/software/mpi-1/Running_OpenMPI.md
index 504db7f2..fd29a09a 100644
--- a/converted/docs.it4i.cz/salomon/software/mpi-1/Running_OpenMPI.md
+++ b/converted/docs.it4i.cz/salomon/software/mpi-1/Running_OpenMPI.md
@@ -5,6 +5,14 @@ Running OpenMPI
+
+
+
+
+
+
+
+
OpenMPI program execution
-------------------------
diff --git a/converted/docs.it4i.cz/salomon/software/mpi-1/mpi.md b/converted/docs.it4i.cz/salomon/software/mpi-1/mpi.md
index 990d65d8..51395ae3 100644
--- a/converted/docs.it4i.cz/salomon/software/mpi-1/mpi.md
+++ b/converted/docs.it4i.cz/salomon/software/mpi-1/mpi.md
@@ -5,6 +5,14 @@ MPI
+
+
+
+
+
+
+
+
Setting up MPI Environment
--------------------------
@@ -141,7 +149,7 @@ scratch /lscratch filesystem.
### Ways to run MPI programs
Optimal way to run an MPI program depends on its memory requirements,
-memory pattern and communication pattern.
+memory access pattern and communication pattern.
Consider these ways to run an MPI program:
1. One MPI process per node, 24 threads per process
@@ -152,13 +160,13 @@ One MPI** process per node, using 24 threads, is most useful for
memory demanding applications, that make good use of processor cache
memory and are not memory bound. This is also a preferred way for
communication intensive applications as one process per node enjoys full
-bandwidth to the network interface.
+bandwidth access to the network interface.
Two MPI** processes per node, using 12 threads each, bound to
processor socket is most useful for memory bandwidth bound applications
such as BLAS1 or FFT, with scalable memory demand. However, note that
-the two processes will share to the network interface. The 12
-threads and socket binding should ensure maximum memory bandwidth
+the two processes will share access to the network interface. The 12
+threads and socket binding should ensure maximum memory access bandwidth
and minimize communication, migration and numa effect overheads.
Important! Bind every OpenMP thread to a core!
diff --git a/converted/docs.it4i.cz/salomon/software/mpi-1/mpi4py-mpi-for-python.md b/converted/docs.it4i.cz/salomon/software/mpi-1/mpi4py-mpi-for-python.md
index fddc6f7d..ce10aacc 100644
--- a/converted/docs.it4i.cz/salomon/software/mpi-1/mpi4py-mpi-for-python.md
+++ b/converted/docs.it4i.cz/salomon/software/mpi-1/mpi4py-mpi-for-python.md
@@ -1,11 +1,23 @@
MPI4Py (MPI for Python)
=======================
+
+
+
+
OpenMPI interface to Python
+
+
+
+
+
+
+
+
Introduction
------------
diff --git a/converted/docs.it4i.cz/salomon/software/numerical-languages/introduction.md b/converted/docs.it4i.cz/salomon/software/numerical-languages/introduction.md
index 5dba41d7..a64bd025 100644
--- a/converted/docs.it4i.cz/salomon/software/numerical-languages/introduction.md
+++ b/converted/docs.it4i.cz/salomon/software/numerical-languages/introduction.md
@@ -1,11 +1,23 @@
Numerical languages
===================
+
+
+
+
Interpreted languages for numerical computations and analysis
+
+
+
+
+
+
+
+
Introduction
------------
@@ -15,7 +27,7 @@ primarily intended for numerical computations.
Matlab
------
-MATLAB^®^ is a high-level language and interactive environment for
+MATLAB®^ is a high-level language and interactive environment for
numerical computation, visualization, and programming.
$ module load MATLAB
diff --git a/converted/docs.it4i.cz/salomon/software/numerical-languages/matlab.md b/converted/docs.it4i.cz/salomon/software/numerical-languages/matlab.md
index 282ebca4..5ac2f70f 100644
--- a/converted/docs.it4i.cz/salomon/software/numerical-languages/matlab.md
+++ b/converted/docs.it4i.cz/salomon/software/numerical-languages/matlab.md
@@ -5,6 +5,14 @@ Matlab
+
+
+
+
+
+
+
+
Introduction
------------
@@ -36,12 +44,12 @@ Matlab on the compute nodes via PBS Pro scheduler.
If you require the Matlab GUI, please follow the general informations
about [running graphical
-applications](../../../get-started-with-it4innovations/ing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html).
+applications](../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html).
Matlab GUI is quite slow using the X forwarding built in the PBS (qsub
-X), so using X11 display redirection either via SSH or directly by
xauth (please see the "GUI Applications on Compute Nodes over VNC" part
-[here](../../../get-started-with-it4innovations/ing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html))
+[here](../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html))
is recommended.
To run Matlab with GUI, use
@@ -94,7 +102,7 @@ code on just a single node.
Following example shows how to start interactive session with support
for Matlab GUI. For more information about GUI based applications on
Anselm see [this
-page](../../../get-started-with-it4innovations/ing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html).
+page](../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html).
$ xhost +
$ qsub -I -v DISPLAY=$(uname -n):$(echo $DISPLAY | cut -d ':' -f 2) -A NONE-0-0 -q qexp -l select=1 -l walltime=00:30:00
@@ -106,7 +114,7 @@ The second part of the command shows how to request all necessary
licenses. In this case 1 Matlab-EDU license and 48 Distributed Computing
Engines licenses.
-Once the to compute nodes is granted by PBS, user can load
+Once the access to compute nodes is granted by PBS, user can load
following modules and start Matlab:
r1i0n17$ module load MATLAB/2015a-EDU
diff --git a/converted/docs.it4i.cz/salomon/software/numerical-languages/octave.md b/converted/docs.it4i.cz/salomon/software/numerical-languages/octave.md
index 22465fc8..8f89df5d 100644
--- a/converted/docs.it4i.cz/salomon/software/numerical-languages/octave.md
+++ b/converted/docs.it4i.cz/salomon/software/numerical-languages/octave.md
@@ -5,6 +5,14 @@ Octave
+
+
+
+
+
+
+
+
GNU Octave is a high-level interpreted language, primarily intended for
numerical computations. It provides capabilities for the numerical
solution of linear and nonlinear problems, and for performing other
diff --git a/converted/docs.it4i.cz/salomon/software/numerical-languages/r.md b/converted/docs.it4i.cz/salomon/software/numerical-languages/r.md
index 58bf5bb8..2044e92d 100644
--- a/converted/docs.it4i.cz/salomon/software/numerical-languages/r.md
+++ b/converted/docs.it4i.cz/salomon/software/numerical-languages/r.md
@@ -5,6 +5,14 @@ R
+
+
+
+
+
+
+
+
Introduction
------------
@@ -34,12 +42,12 @@ Modules
-------
**The R version 3.1.1 is available on the cluster, along with GUI
-interface Rstudio**
+interface Rstudio
Application Version module
------------- -------------- ---------------------
R** R 3.1.1 R/3.1.1-intel-2015b
-Rstudio**** Rstudio 0.97 Rstudio
+Rstudio** Rstudio 0.97 Rstudio
$ module load R
@@ -55,10 +63,10 @@ OMP_NUM_THREADS environment variable.
### Interactive execution
-To run R interactively, using Rstudio** GUI, log in with ssh -X parameter
+To run R interactively, using Rstudio GUI, log in with ssh -X parameter
for X11 forwarding. Run rstudio:
- $ module load Rstudio**
+ $ module load Rstudio
$ rstudio
### Batch execution
@@ -397,7 +405,7 @@ The above is the mpi.apply MPI example for calculating the number π.
Only the slave processes carry out the calculation. Note the
mpi.parSapply(), ** function call. The package
parallel
-[example](r.html#package-parallel)[above](r.html#package-parallel)
+[example](r.html#package-parallel)[above](r.html#package-parallel){.anchor
may be trivially adapted (for much better performance) to this structure
using the mclapply() in place of mpi.parSapply().
@@ -452,6 +460,10 @@ and general [MPI](../mpi-1.html) sections.
+
+
+
+
Xeon Phi Offload
----------------
@@ -464,3 +476,11 @@ environment variable before R execution :
[Read more about automatic
offload](../intel-xeon-phi.html)
+
+
+
+
+
+
+
+
diff --git a/converted/docs.it4i.cz/salomon/software/operating-system.md b/converted/docs.it4i.cz/salomon/software/operating-system.md
index 12519fd4..ea183352 100644
--- a/converted/docs.it4i.cz/salomon/software/operating-system.md
+++ b/converted/docs.it4i.cz/salomon/software/operating-system.md
@@ -1,11 +1,23 @@
Operating System
================
+
+
+
+
The operating system, deployed on Salomon cluster
+
+
+
+
+
+
+
+
The operating system on Salomon is Linux - CentOS 6.6.
>The CentOS Linux distribution is a stable, predictable, manageable
diff --git a/converted/docs.it4i.cz/salomon/storage/cesnet-data-storage.md b/converted/docs.it4i.cz/salomon/storage/cesnet-data-storage.md
index be82b6fa..1f006bd5 100644
--- a/converted/docs.it4i.cz/salomon/storage/cesnet-data-storage.md
+++ b/converted/docs.it4i.cz/salomon/storage/cesnet-data-storage.md
@@ -5,6 +5,14 @@ CESNET Data Storage
+
+
+
+
+
+
+
+
Introduction
------------
@@ -23,7 +31,7 @@ Republic.
User of data storage CESNET (DU) association can become organizations or
an individual person who is either in the current employment
relationship (employees) or the current study relationship (students) to
-a legal entity (organization) that meets the “Principles for to
+a legal entity (organization) that meets the “Principles for access to
CESNET Large infrastructure (Access Policy)”.
User may only use data storage CESNET for data transfer and storage
@@ -37,12 +45,12 @@ The service is documented at
please contact directly CESNET Storage Department via e-mail
[du-support(at)cesnet.cz](mailto:du-support@cesnet.cz).
-The procedure to obtain the CESNET is quick and trouble-free.
+The procedure to obtain the CESNET access is quick and trouble-free.
(source
[https://du.cesnet.cz/](https://du.cesnet.cz/wiki/doku.php/en/start "CESNET Data Storage"))
-CESNET storage
+CESNET storage access
---------------------
### Understanding Cesnet storage
@@ -51,7 +59,7 @@ It is very important to understand the Cesnet storage before uploading
data. Please read
<https://du.cesnet.cz/en/navody/home-migrace-plzen/start> first.
-Once registered for CESNET Storage, you may [ the
+Once registered for CESNET Storage, you may [access the
storage](https://du.cesnet.cz/en/navody/faq/start) in
number of ways. We recommend the SSHFS and RSYNC methods.
@@ -59,7 +67,7 @@ number of ways. We recommend the SSHFS and RSYNC methods.
SSHFS: The storage will be mounted like a local hard drive
-The SSHFS provides a very convenient way to the CESNET Storage.
+The SSHFS provides a very convenient way to access the CESNET Storage.
The storage will be mounted onto a local directory, exposing the vast
CESNET Storage as if it was a local removable harddrive. Files can be
than copied in and out in a usual fashion.
@@ -74,7 +82,7 @@ Mount tier1_home **(only 5120M !)**:
$ sshfs username@ssh.du1.cesnet.cz:. cesnet/
-For easy future from Anselm, install your public key
+For easy future access from Anselm, install your public key
$ cp .ssh/id_rsa.pub cesnet/.ssh/authorized_keys
@@ -92,7 +100,7 @@ Once done, please remember to unmount the storage
$ fusermount -u cesnet
-### Rsync
+### Rsync access
Rsync provides delta transfer for best performance, can resume
interrupted transfers
@@ -127,3 +135,7 @@ in the Storage VO
$ rsync --progress -av username@ssh.du1.cesnet.cz:VO_storage-cache_tape/datafolder .
Transfer rates of about 28MB/s can be expected.
+
+
+
+
diff --git a/converted/docs.it4i.cz/salomon/storage/storage.md b/converted/docs.it4i.cz/salomon/storage/storage.md
index 8cd9de88..fd56abed 100644
--- a/converted/docs.it4i.cz/salomon/storage/storage.md
+++ b/converted/docs.it4i.cz/salomon/storage/storage.md
@@ -5,6 +5,14 @@ Storage
+
+
+
+
+
+
+
+
Introduction
------------
@@ -13,7 +21,7 @@ There are two main shared file systems on Salomon cluster, the [
HOME](storage.html#home)
and [
SCRATCH](storage.html#shared-filesystems).
-All login and compute nodes may same data on shared filesystems.
+All login and compute nodes may access same data on shared filesystems.
Compute nodes are also equipped with local (non-shared) scratch, ramdisk
and tmp filesystems.
@@ -48,7 +56,7 @@ SCRATCH filesystem is partitioned to [WORK and TEMP
workspaces](storage.html#shared-workspaces). The HOME
filesystem is realized as a tiered NFS disk storage. The SCRATCH
filesystem is realized as a parallel Lustre filesystem. Both shared file
-systems are ible via the Infiniband network. Extended ACLs are
+systems are accessible via the Infiniband network. Extended ACLs are
provided on both HOME/SCRATCH filesystems for the purpose of sharing
data with other users using fine-grained control.
@@ -105,7 +113,7 @@ round-robin fashion to ensure load balancing.
When a client (a compute
node from your job) needs to create
-or a file, the client queries the metadata server (
+or access a file, the client queries the metadata server (
MDS) and the metadata target (
MDT) for the layout and location of the
[file's
@@ -144,7 +152,7 @@ significantly impact the I/O performance you experience.
Use the lfs getstripe for getting the stripe parameters. Use the lfs
setstripe command for setting the stripe parameters to get optimal I/O
performance The correct stripe setting depends on your needs and file
- patterns.
+access patterns.
```
$ lfs getstripe dir|filename
@@ -185,7 +193,7 @@ When multiple processes are writing blocks of data to the same file in
parallel, the I/O performance for large files will improve when the
stripe_count is set to a larger value. The stripe count sets the number
of OSTs the file will be written to. By default, the stripe count is set
-to 1. While this default setting provides for efficient of
+to 1. While this default setting provides for efficient access of
metadata (for example to support the ls -l command), large files should
use stripe counts of greater than 1. This will increase the aggregate
I/O bandwidth by using multiple OSTs in parallel instead of just one. A
@@ -197,10 +205,10 @@ of the number of processes performing the write in parallel, so that you
achieve load balance among the OSTs. For example, set the stripe count
to 16 instead of 15 when you have 64 processes performing the writes.
-Using a large stripe size can improve performance when ing very
+Using a large stripe size can improve performance when accessing very
large files
-Large stripe size allows each client to have exclusive to its own
+Large stripe size allows each client to have exclusive access to its own
part of a file. However, it can be counterproductive in some cases if it
does not match your I/O pattern. The choice of stripe size has no effect
on a single-stripe file.
@@ -293,7 +301,7 @@ number of named user and named group entries.
ACLs on a Lustre file system work exactly like ACLs on any Linux file
system. They are manipulated with the standard tools in the standard
-manner. Below, we create a directory and allow a specific user .
+manner. Below, we create a directory and allow a specific user access.
```
[vop999@login1.salomon ~]$ umask 027
@@ -377,11 +385,11 @@ The WORK workspace resides on SCRATCH filesystem. Users may create
subdirectories and files in directories **/scratch/work/user/username**
and **/scratch/work/project/projectid. **The /scratch/work/user/username
is private to user, much like the home directory. The
-/scratch/work/project/projectid is ible to all users involved in
+/scratch/work/project/projectid is accessible to all users involved in
project projectid. >
The WORK workspace is intended to store users project data as well as
-for high performance to input and output files. All project data
+for high performance access to input and output files. All project data
should be removed once the project is finished. The data on the WORK
workspace are not backed up.
@@ -417,7 +425,7 @@ Lustre
### TEMP
The TEMP workspace resides on SCRATCH filesystem. The TEMP workspace
-point is /scratch/temp. Users may freely create subdirectories
+accesspoint is /scratch/temp. Users may freely create subdirectories
and files on the workspace. Accessible capacity is 1.6P, shared among
all users on TEMP and WORK. Individual users are restricted by
filesystem usage quotas, set to 100TB per user. The purpose of this
@@ -428,14 +436,14 @@ insufficient for particular user, please contact
lifted upon request.
The TEMP workspace is intended for temporary scratch data generated
-during the calculation as well as for high performance to input
+during the calculation as well as for high performance access to input
and output files. All I/O intensive jobs must use the TEMP workspace as
their working directory.
Users are advised to save the necessary data from the TEMP workspace to
HOME or WORK after the calculations and clean up the scratch files.
-Files on the TEMP filesystem that are **not ed for more than 90
+Files on the TEMP filesystem that are **not accessed for more than 90
days** will be automatically **deleted**.
The TEMP workspace is hosted on SCRATCH filesystem. The SCRATCH is
@@ -471,16 +479,16 @@ RAM disk
Every computational node is equipped with filesystem realized in memory,
so called RAM disk.
-Use RAM disk in case you need really fast to your data of limited
+Use RAM disk in case you need really fast access to your data of limited
size during your calculation.
Be very careful, use of RAM disk filesystem is at the expense of
operational memory.
-The local RAM disk is mounted as /ramdisk and is ible to user
+The local RAM disk is mounted as /ramdisk and is accessible to user
at /ramdisk/$PBS_JOBID directory.
The local RAM disk filesystem is intended for temporary scratch data
-generated during the calculation as well as for high performance
+generated during the calculation as well as for high performance access
to input and output files. Size of RAM disk filesystem is limited. Be
very careful, use of RAM disk filesystem is at the expense of
operational memory. It is not recommended to allocate large amount of
@@ -525,4 +533,12 @@ Mountpoint Usage
/ramdisk job temporary data, node local local 120GB 90 GB/s none Compute nodes purged after job ends
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+
+
+
+
+
+
+
+
diff --git a/html_md.sh b/html_md.sh
index cb24f7b7..b9ee31f4 100755
--- a/html_md.sh
+++ b/html_md.sh
@@ -2,117 +2,59 @@
### DOWNLOAD AND CONVERT DOCUMENTATION
# autor: kru0052
-# version: 0.36
-# change: repair images bugs and add new filtering html and css elements
+# version: 0.4
+# change: repair bugs and optimalizations
# bugs: bad formatting tables, bad links for other files, stayed a few html elements, formatting bugs...
###
if [ "$1" = "-t" ]; then
# testing new function
- echo "Testing 1..."
-
- rm -rf ./converted
-
- # exists file for move?
- if [ -f ./info/list_md.txt ];
- then
- mkdir converted;
- (while read i;
- do
- mkdir "./converted/$i";
- done) < ./source/list_folder.txt
-
- # move md files to new folders
- while read a b ; do
- cp "$a" "./converted/$b";
-
- done < <(paste ./info/list_md.txt ./source/list_md_mv.txt)
- # copy jpg and jpeg to new folders
-
- #cat "${i%.*}TMP.md" > "${i%.*}.md";
-
- while read a b ; do cp "$a" "./converted/$b"; done < <(paste ./info/list_image.txt ./source/list_image_mv.txt)
-
- cp ./docs.it4i.cz/salomon/salomon ./converted/docs.it4i.cz/salomon/salomon
- cp ./docs.it4i.cz/salomon/salomon-2 ./converted/docs.it4i.cz/salomon/salomon-2
- cp ./converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/fairshare_formula.png ./converted/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/fairshare_formula.png
- cp ./converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/job_sort_formula.png ./converted/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job_sort_formula.png
- cp ./converted/docs.it4i.cz/salomon/software/debuggers/vtune-amplifier.png ./converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/vtune-amplifier.png
- cp ./converted/docs.it4i.cz/salomon/software/debuggers/Snmekobrazovky20160708v12.33.35.png ./converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/Snmekobrazovky20160708v12.33.35.png
-
- wget https://docs.it4i.cz/anselm-cluster-documentation/software/virtualization/virtualization-job-workflow
- mv ./virtualization-job-workflow ./converted/docs.it4i.cz/anselm-cluster-documentation/software/
- wget https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/images/fig6.png
- mv ./fig6.png ./converted/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/fig6.png
- wget https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/images/fig5.png
- mv ./fig5.png ./converted/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/fig5.png
- wget https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/images/fig1.png
- mv ./fig1.png ./converted/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/fig1.png
- wget https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/images/fig2.png
- mv ./fig2.png ./converted/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/fig2.png
- wget https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/images/fig4.png
- mv ./fig4.png ./converted/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/fig4.png
- wget https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/images/fig3.png
- mv ./fig3.png ./converted/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/fig3.png
-
-
-
- else
- echo "list_md.txt not exists!!!!!"
- fi
-
-
-fi
-if [ "$1" = "-t1" ]; then
- # testing new function
-
- echo "Testing 1..."
-
-
- while read a ; do
-
- echo "$a";
-
- sed -e 's/``` /```/' "./converted/$a" | sed -e 's/ //' | sed -e 's/<span class="pln">//' | sed -e 's/<span//' | sed -e 's/class="pln">//' | sed -e 's/<\/span>//' | sed -e 's/^\*\*//' | sed -e 's/\^\[>\[1<span>\]<\/span>\]//' > "./converted/${a%.*}TMP.md";
-
- while read x ; do
- arg1=`echo "$x" | cut -d"&" -f1 | sed 's:[]\[\^\$\.\*\/\"]:\\\\&:g'`;
- arg2=`echo $x | cut -d"&" -f2 | sed 's:[]\[\^\$\.\*\/\"]:\\\\&:g'`;
- #echo "$arg1";
- #echo ">$arg2";
-
- sed -e 's/'"$arg1"'/'"$arg2"'/' "./converted/${a%.*}TMP.md" > "./converted/${a%TMP.*}.TEST.md";
- cat "./converted/${a%TMP.*}.TEST.md" > "./converted/${a%.*}TMP.md";
- done < ./source/replace.txt
- cat "./converted/${a%.*}TMP.md" > "./converted/${a%.*}.md";
- rm "./converted/${a%.*}TMP.md";
- rm "./converted/${a%TMP.*}.TEST.md";
- done <./source/list_md_mv.txt
-
-
fi
if [ "$1" = "-w" ]; then
# download html pages
wget -X pbspro-documentation,changelog,whats-new,portal_css,portal_javascripts,++resource++jquery-ui-themes,anselm-cluster-documentation/icon.jpg -R favicon.ico,pdf.png,logo.png,background.png,application.png,search_icon.png,png.png,sh.png,touch_icon.png,anselm-cluster-documentation/icon.jpg,*js,robots.txt,*xml,RSS,download_icon.png,pdf,*zip,*rar,@@*,anselm-cluster-documentation/icon.jpg.1 --mirror --convert-links --adjust-extension --page-requisites --no-parent https://docs.it4i.cz;
- wget http://verif.cs.vsb.cz/aislinn/doc/report.png
- mv report.png ./converted/salomon/software/debuggers/
+ wget --directory-prefix=./docs.it4i.cz/ http://verif.cs.vsb.cz/aislinn/doc/report.png
+ wget --directory-prefix=./docs.it4i.cz/ https://docs.it4i.cz/anselm-cluster-documentation/software/virtualization/virtualization-job-workflow
+ wget --directory-prefix=./docs.it4i.cz/ https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/images/fig1.png
+ wget --directory-prefix=./docs.it4i.cz/ https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/images/fig2.png
+ wget --directory-prefix=./docs.it4i.cz/ https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/images/fig3.png
+ wget --directory-prefix=./docs.it4i.cz/ https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/images/fig4.png
+ wget --directory-prefix=./docs.it4i.cz/ https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/images/fig5.png
+ wget --directory-prefix=./docs.it4i.cz/ https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/images/fig6.png
+
fi
if [ "$1" = "-c" ]; then
### convert html to md
# erasing the previous transfer
+
rm -rf converted;
rm -rf info;
+ # erasing duplicate files and unwanted files
+ (while read i;
+ do
+ if [ -f "$i" ];
+ then
+ echo "$(tput setaf 9)$i deleted";
+ rm "$i";
+ fi
+
+ done) < ./source/list_rm
+
+ counter=1
+ count=$(find . -name "*.html" -type f | wc -l)
+
find . -name "*.ht*" |
while read i;
do
# first filtering html
- echo "$i";
- printf "\t\tfiltering html files...\n";
+ echo "$(tput setaf 12)($counter/$count)$(tput setaf 11)$i";
+ counter=$((counter+1))
+ printf "$(tput setaf 15)\t\tfirst filtering html files...\n";
HEAD=$(grep -n -m1 '<h1' "$i" |cut -f1 -d: | tr --delete '\n')
END=$(grep -n -m1 '<!-- <div tal:content=' "$i" |cut -f1 -d: | tr --delete '\n')
@@ -126,49 +68,42 @@ if [ "$1" = "-c" ]; then
pandoc -f html -t markdown+pipe_tables-grid_tables "${i%.*}TMP.html" -o "${i%.*}.md";
rm "${i%.*}TMP.html";
- # create filter_auto (css, html, ...)
- grep -o -P '(?<={).*(?=})' "${i%.*}.md" | sort -u | sed '/{/d' | sed '/\$/d' >> filter_auto;
- sort -u filter_auto -o filter_auto;
-
- # exceptions filter_auto
- (while read y;
- do
- # search and delete according with filter_auto
- sed -e 's/'"$y"'//g' filter_auto > filter_autoTMP;
- cat filter_autoTMP > filter_auto;
- done) < ./source/exceptions_filter_auto
-
- # text filtering of html, css, ...
- printf "\t\tautomatic filter...\n"
- (while read y;
- do
- # search and delete according with filter_auto and erase unwanted elements
- sed -e 's/{'"$y"'}//g' "${i%.*}.md" | sed -e 's/\\//g' | sed -e 's/^: //g' | sed -e 's/<\/div>//g' | sed '/^<div/d' | sed -e 's/^Obsah//g' | sed -e 's/{#putty---before-we-start-//g' | sed -e 's/ssh-connection style="text-alignstart; "}//g'| awk -v RS='\n\n\n\n\n' 1 > "${i%.*}TMP.md";
- cat "${i%.*}TMP.md" > "${i%.*}.md";
- done) < filter_auto
-
+ # second filtering html and css elements...
+ printf "\t\tsecond filtering html and css elements...\n"
+ sed -e 's/``` /```/' "${i%.*}.md" | sed -e 's/ //' | sed -e 's/<\/div>//g' | sed '/^<div/d' | sed -e 's/<\/span>//' | sed -e 's/^\*\*//' | sed -e 's/\\//g' | sed -e 's/^: //g' | sed -e 's/^Obsah//g' > "${i%.*}TMP.md";
+ while read x ; do
+ arg1=`echo "$x" | cut -d"&" -f1 | sed 's:[]\[\^\$\.\*\/\"]:\\\\&:g'`;
+ arg2=`echo "$x" | cut -d"&" -f2 | sed 's:[]\[\^\$\.\*\/\"]:\\\\&:g'`;
+
+ sed -e 's/'"$arg1"'/'"$arg2"'/' "${i%.*}TMP.md" > "${i%.*}TMP.TEST.md";
+ cat "${i%.*}TMP.TEST.md" > "${i%.*}TMP.md";
+ done < ./source/replace
+
+ # repair image...
+ printf "\t\trepair images...\n"
+ while read x ; do
+ arg1=`echo "$x" | cut -d"&" -f1 | sed 's:[]\[\^\$\.\*\/\"]:\\\\&:g'`;
+ arg2=`echo "$x" | cut -d"&" -f2 | sed 's:[]\[\^\$\.\*\/\"]:\\\\&:g'`;
+
+ sed -e 's/'"$arg1"'/'"$arg2"'/' "${i%.*}TMP.md" > "${i%.*}.md";
+ cat "${i%.*}.md" > "${i%.*}TMP.md";
+ done < ./source/repairIMG
+
+ cat "${i%.*}TMP.md" > "${i%.*}.md";
+
# delete temporary files
- rm "${i%.*}TMP.md";
+ rm "${i%.*}TMP.md";
+ rm "${i%.*}TMP.TEST.md";
done
- # delete empty files, duplicate files and unwanted files
+ # delete empty files
find -type f -size -10c |
while read i;
do
rm "$i";
- echo "$i deleted";
+ echo "$(tput setaf 9)$i deleted";
done
- rm filter_autoTMP
- rm filter_auto
- (while read i;
- do
- if [ -f "$i" ];
- then
- rm "$i";
- fi
-
- done) < ./source/list_rm.txt
### create new folder and move converted files
# create folder info and view all files and folder
@@ -179,20 +114,29 @@ if [ "$1" = "-c" ]; then
find ./docs.it4i.cz -name "*.md" -type f> ./info/list_md.txt;
find ./docs.it4i.cz -type d | sort > ./info/list_folder.txt
- # exists file for move?
- if [ -f ./info/list_md.txt ];
- then
- mkdir converted;
- (while read i;
- do
- mkdir "./converted/$i";
- done) < ./source/list_folder.txt
-
- # move md files to new folders
- while read a b ; do cp "$a" "./converted/$b"; done < <(paste ./info/list_md.txt ./source/list_md_mv.txt)
- # copy jpg and jpeg to new folders
- while read a b ; do cp "$a" "./converted/$b"; done < <(paste ./info/list_image.txt ./source/list_image_mv.txt)
- else
- echo "list_md.txt not exists!!!!!"
- fi
+ rm -rf ./converted
+
+ mkdir converted;
+ (while read i;
+ do
+ mkdir "./converted/$i";
+ done) < ./source/list_folder
+
+ # move md files to new folders
+ while read a b ; do
+ cp "$a" "./converted/$b";
+ done < <(paste ./info/list_md.txt ./source/list_md_mv)
+
+ # copy jpg and jpeg to new folders
+ while read a b ; do
+ cp "$a" "./converted/$b";
+ done < <(paste ./info/list_image.txt ./source/list_image_mv.txt)
+ cp ./docs.it4i.cz/salomon/salomon ./converted/docs.it4i.cz/salomon/salomon
+ cp ./docs.it4i.cz/salomon/salomon-2 ./converted/docs.it4i.cz/salomon/salomon-2
+ cp ./converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/fairshare_formula.png ./converted/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/fairshare_formula.png
+ cp ./converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/job_sort_formula.png ./converted/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job_sort_formula.png
+ cp ./converted/docs.it4i.cz/salomon/software/debuggers/vtune-amplifier.png ./converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/vtune-amplifier.png
+ cp ./converted/docs.it4i.cz/salomon/software/debuggers/Snmekobrazovky20160708v12.33.35.png ./converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/Snmekobrazovky20160708v12.33.35.png
+ cp ./docs.it4i.cz/virtualization-job-workflow ./converted/docs.it4i.cz/anselm-cluster-documentation/software/
+
fi
diff --git a/source/exceptions_filter_auto b/source/exceptions_filter_auto
deleted file mode 100644
index bbdc8036..00000000
--- a/source/exceptions_filter_auto
+++ /dev/null
@@ -1,18 +0,0 @@
-00001..00111
-#10-after-you-end-your-visualization-session
-#1-connect-to-a-login-node
-#1-in-your-vnc-session-open-a-terminal-and-allocate-a-node-using-pbspro-qsub-command
-#2-in-your-vnc-session-open-another-terminal-keep-the-one-with-interactive-pbspro-job-open
-#2-run-your-own-instance-of-turbovnc-server
-#3-load-the-virtualgl-module
-#3-remember-which-display-number-your-vnc-server-runs-you-will-need-it-in-the-future-to-stop-the-server
-#4-remember-the-exact-login-node-where-your-vnc-server-runs
-#4-run-your-desired-opengl-accelerated-application-using-virtualgl-script-vglrun
-#5-after-you-end-your-work-with-the-opengl-application
-#5-remember-on-which-tcp-port-your-own-vnc-server-is-running
-#6-connect-to-the-login-node-where-your-vnc-server-runs-with-ssh-to-tunnel-your-vnc-session
-#7-if-you-don-t-have-turbo-vnc-installed-on-your-workstation
-#8-run-turbovnc-viewer-from-your-workstation
-#9-proceed-to-the-chapter-access-the-visualization-node
-PBS_ARRAY_INDEX
-IDX
diff --git a/source/list_folder.txt b/source/list_folder
similarity index 100%
rename from source/list_folder.txt
rename to source/list_folder
diff --git a/source/list_image_mv b/source/list_image_mv
new file mode 100644
index 00000000..d7335c8e
--- /dev/null
+++ b/source/list_image_mv
@@ -0,0 +1,98 @@
+./docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/fig2.png
+./docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/fig5.png
+./docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/fig6.png
+./docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/fig3.png
+./docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/TightVNC_login.png
+./docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/putty-tunnel.png
+./docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/gnome-terminal.png
+./docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/gdmscreensaver.png
+./docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/gnome-compute-nodes-over-vnc.png
+./docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/gdmdisablescreensaver.png
+./docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/cygwinX11forwarding.png
+./docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/XWinlistentcp.png
+./docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/PuttyKeygenerator_004V.png
+./docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/20150312_143443.png
+./docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/PageantV.png
+./docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/PuttyKeygenerator_001V.png
+./docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/PuTTY_host_Salomon.png
+./docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/PuTTY_keyV.png
+./docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/PuttyKeygenerator_005V.png
+./docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/PuTTY_save_Salomon.png
+./docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/PuttyKeygeneratorV.png
+./docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/PuTTY_open_Salomon.png
+./docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/PuttyKeygenerator_002V.png
+./docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/PuttyKeygenerator_006V.png
+./docs.it4i.cz/salomon/accessing-the-cluster/copy_of_vpn_web_install_3.png
+./docs.it4i.cz/salomon/accessing-the-cluster/vpn_contacting.png
+./docs.it4i.cz/salomon/resource-allocation-and-job-execution/rswebsalomon.png
+./docs.it4i.cz/salomon/accessing-the-cluster/vpn_successfull_connection.png
+./docs.it4i.cz/salomon/accessing-the-cluster/vpn_web_install_2.png
+./docs.it4i.cz/salomon/accessing-the-cluster/vpn_web_login_2.png
+./docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/gnome_screen.png
+./docs.it4i.cz/salomon/network-1/IBsingleplanetopologyAcceleratednodessmall.png
+./docs.it4i.cz/salomon/network-1/IBsingleplanetopologyICEXMcellsmall.png
+./docs.it4i.cz/salomon/network-1/Salomon_IB_topology.png
+./docs.it4i.cz/salomon/network-1/7D_Enhanced_hypercube.png
+./docs.it4i.cz/salomon/accessing-the-cluster/vpn_web_login.png
+./docs.it4i.cz/salomon/accessing-the-cluster/vpn_login.png
+./docs.it4i.cz/salomon/software/debuggers/totalview2.png
+./docs.it4i.cz/salomon/software/debuggers/Snmekobrazovky20160211v14.27.45.png
+./docs.it4i.cz/salomon/software/debuggers/ddt1.png
+./docs.it4i.cz/salomon/software/debuggers/totalview1.png
+./docs.it4i.cz/salomon/software/debuggers/Snmekobrazovky20160708v12.33.35.png
+./docs.it4i.cz/salomon/software/intel-suite/Snmekobrazovky20151204v15.35.12.png
+./docs.it4i.cz/salomon/software/ansys/AMsetPar1.png
+./docs.it4i.cz/salomon/accessing-the-cluster/vpn_contacting_https_cluster.png
+./docs.it4i.cz/salomon/accessing-the-cluster/vpn_web_download.png
+./docs.it4i.cz/salomon/accessing-the-cluster/vpn_web_download_2.png
+./docs.it4i.cz/salomon/accessing-the-cluster/vpn_contacting_https.png
+./docs.it4i.cz/salomon/accessing-the-cluster/vpn_web_install_4.png
+./docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vncviewer.png
+./docs.it4i.cz/salomon/resource-allocation-and-job-execution/job_sort_formula.png
+./docs.it4i.cz/salomon/resource-allocation-and-job-execution/fairshare_formula.png
+./docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/rsweb.png
+./docs.it4i.cz/anselm-cluster-documentation/quality2.png
+./docs.it4i.cz/anselm-cluster-documentation/turbovncclientsetting.png
+./docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials/Authorization_chain.png
+./docs.it4i.cz/anselm-cluster-documentation/scheme.png
+./docs.it4i.cz/anselm-cluster-documentation/quality3.png
+./docs.it4i.cz/anselm-cluster-documentation/legend.png
+./docs.it4i.cz/anselm-cluster-documentation/bullxB510.png
+./docs.it4i.cz/salomon/software/debuggers/vtune-amplifier.png
+./docs.it4i.cz/anselm-cluster-documentation/software/debuggers/totalview2.png
+./docs.it4i.cz/anselm-cluster-documentation/software/debuggers/Snmekobrazovky20141204v12.56.36.png
+./docs.it4i.cz/anselm-cluster-documentation/software/debuggers/ddt1.png
+./docs.it4i.cz/anselm-cluster-documentation/software/debuggers/totalview1.png
+./docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/Matlab.png
+./docs.it4i.cz/anselm-cluster-documentation/quality1.png
+./docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/fig1.png
+./docs.it4i.cz/salomon/software/debuggers/report.png
+./docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vpnuiV.png
+./docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/fig4.png
+./docs.it4i.cz/salomon/software/ansys/Fluent_Licence_2.jpg
+./docs.it4i.cz/salomon/software/ansys/Fluent_Licence_4.jpg
+./docs.it4i.cz/salomon/software/ansys/Fluent_Licence_1.jpg
+./docs.it4i.cz/salomon/software/ansys/Fluent_Licence_3.jpg
+./docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/Anselmprofile.jpg
+./docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/anyconnecticon.jpg
+./docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/anyconnectcontextmenu.jpg
+./docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/logingui.jpg
+./docs.it4i.cz/anselm-cluster-documentation/software/ansys/Fluent_Licence_2.jpg
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index bb78bf58..24506781 100644
--- a/source/list_image_mv.txt
+++ b/source/list_image_mv.txt
@@ -1,3 +1,7 @@
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new file mode 100644
index 00000000..f3705ba1
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+operation.](images/fig3.png "fig3.png")&operation.](fig3.png "fig3.png")&
+where the position is ambiguous.](images/fig4.png)&where the position is ambiguous.](fig4.png)
+genomic coordinates.](images/fig6.png.1 "fig6.png")&genomic coordinates.](fig6.png.1 "fig6.png")
+ [](cygwin-and-x11-forwarding.html)&
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diff --git a/source/replace b/source/replace
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+ []()&
+ **[]()&**
+- - &
+.[]()&.
+### []()[]()&###
+### []()&###
+### **&###
+style="text-align: left; float: none; ">&
+class="anchor-link">&
+class="Apple-converted-space">&
+class="discreet visualHighlight">&
+class="emphasis">&
+class="glossaryItem">&
+class="highlightedSearchTerm">&
+class="highlightedSearchTerm">SSH</span><span>&highlightedSearchTerm
+class="hps">&
+class="hps">&
+class="hps">More</span> <span class="hps">&
+class="hps trans-target-highlight">&
+class="internal-link">&
+class="internal-link"><span id="result_box" class="short_text"><span&
+class="monospace">&
+class="monospace">LAPACKE</span> module, which includes Intel's LAPACKE&LAPACKE modelu, which includes Intel's LAPACKE
+class="n">&
+### class="n">&###
+class="n">&
+class="pre">&
+class="pun">node_group_key&
+class="short_text"><span&
+class="smarterwiki-popup-bubble-body"><span&
+class="smarterwiki-popup-bubble-links-container"><span&
+class="smarterwiki-popup-bubble-links-row">[{.smarterwiki-popup-bubble-link-favicon}](http://maps.google.com/maps?q=HDF5%20icc%20serial%09pthread%09hdf5%2F1.8.13%09%24HDF5_INC%20%24HDF5_SHLIB%09%24HDF5_INC%20%24HDF5_CPP_LIB%09%24HDF5_INC%20%24HDF5_F90_LIB%0A%0AHDF5%20icc%20parallel%20MPI%0A%09pthread%2C%20IntelMPI%09hdf5-parallel%2F1.8.13%09%24HDF5_INC%20%24HDF5_SHLIB%09Not%20supported%09%24HDF5_INC%20%24HDF5_F90_LIB "Search Google Maps"){.smarterwiki-popup-bubble-link}[{.smarterwiki-popup-bubble-link-favicon}](http://www.google.com/search?q=HDF5%20icc%20serial%09pthread%09hdf5%2F1.8.13%09%24HDF5_INC%20%24HDF5_SHLIB%09%24HDF5_INC%20%24HDF5_CPP_LIB%09%24HDF5_INC%20%24HDF5_F90_LIB%0A%0AHDF5%20icc%20parallel%20MPI%0A%09pthread%2C%20IntelMPI%09hdf5-parallel%2F1.8.13%09%24HDF5_INC%20%24HDF5_SHLIB%09Not%20supported%09%24HDF5_INC%20%24HDF5_F90_LIB "Search Google"){.smarterwiki-popup-bubble-link}[](http://www.google.com/search?hl=com&btnI=I'm+Feeling+Lucky&q=HDF5%20icc%20serial%09pthread%09hdf5%2F1.8.13%09%24HDF5_INC%20%24HDF5_SHLIB%09%24HDF5_INC%20%24HDF5_CPP_LIB%09%24HDF5_INC%20%24HDF5_F90_LIB%0A%0AHDF5%20icc%20parallel%20MPI%0A%09pthread%2C%20IntelMPI%09hdf5-parallel%2F1.8.13%09%24HDF5_INC%20%24HDF5_SHLIB%09Not%20supported%09%24HDF5_INC%20%24HDF5_F90_LIB+wikipedia "Search Wikipedia"){.smarterwiki-popup-bubble-link}</span></span></span></span></span>&
+class="smarterwiki-popup-bubble-links"><span&
+class="smarterwiki-popup-bubble smarterwiki-popup-bubble-active smarterwiki-popup-bubble-flipped"><span&&
+class="smarterwiki-popup-bubble-tip"></span><span
+</div>&
+<div>&
+<div class="itemizedlist">&
+<div id="d4841e18">&
+<div id="d4841e21">&
+<div id="d4841e24">&
+<div id="d4841e27">&
+<div id="d4841e30">&
+<div id="d4841e34">&
+<div id="d4841e37">&
+{.external&
+### Gnome on Windows**&### Gnome on Windows
+### Notes **&### Notes
+</span>&
+<span&
+[<span class="anchor-link">&
+<span class="discreet">&
+<span class="discreet"></span>&
+<span class="glossaryItem">&
+<span class="hps">&
+<span class="hps alt-edited">&
+<span class="listitem">&
+<span class="n">&
+<span class="s1">&
+<span class="WYSIWYG_LINK">&
+<span dir="auto">&
+<span id="__caret">&
+<span id="__caret"><span id="__caret"></span></span>&
+(<span id="result_box">&
+<span id="result_box" class="short_text"><span class="hps">&
+<span id="result_box"><span class="hps">&
+</span></span>&
+</span> <span&
+<span><span>&
+</span> <span class="hps">&
+</span> <span class="hps">who have a valid</span> <span&
+<span><span class="monospace">&
+<span><span>Introduction&###Introduction
+</span></span><span><span>&
+</span></span></span></span><span><span>&
+</span></span><span><span><span><span>&
+.<span style="text-align: left; "> </span>&
+<span style="text-align: start; ">&
+{.state-missing-value
+ style="text-align: left; float: none; ">&
+ style="text-align: left; float: none; ">&
+ style="text-align: left; float: none; ">change it&change it to
+ style="text-align: left; float: none; ">Check Putty settings:&
+ style="text-align: left; float: none; ">Enable X11&Enable X11
+ style="text-align: left; float: none; "> &
+style="text-align: start; ">&
+style="text-align: start; float: none; ">&
+**Summary&**Summary**
+Tape Library T950B**&**Tape Library T950B**
+.text}.&
+.text}&
+ ****The R version 3.0.1 is available on Anselm, along with GUI interface&**The R version 3.0.1 is available on Anselm, along with GUI interface
+ssh-connection style="text-alignstart; "}&
+<div&
+</div>&
+{.anchor-link}&
+{.code-basic style="text-align: start; "}&
+{.code .highlight .white .shell}&
+{.docutils .literal}&
+{.email-link}&
+{.external-link}&
+{.fragment}&
+{.image-inline}&
+{.image-inline width="451" height="513"}&
+{.internal-link}&
+{.literal-block}&
+{.mw-redirect}&
+{#parent-fieldname-title}&
+{#parent-fieldname-title .documentFirstHeading}&
+{.prettyprint}&
+{.prettyprint .lang-cpp}&
+{.prettyprint .lang-sh}&
+{.prettyprint .lang-sh .prettyprinted}&
+{#putty---before-we-start-ssh-connection style="text-align: start; "}&
+{#resources-allocation-policy}&
+{#schematic-overview}&
+{.screen}&
+{#setup-and-start-your-own-turbovnc-server}&
+{style="text-align: left; "}&
+ssh-connection style="text-alignstart; "}&
+{#putty---before-we-start-&
+<span class="pln">&
+class="pln">&
+id="parent-fieldname-text-5739e5d4b93b40a6b3d987bd4047d4e0">&
+id="content-core">&
+id="viewlet-above-content-body">&
+id="viewlet-below-content-title">&
+^[>[1<span>]]&
+^&
+-link}&
+<span&
+Input:** FASTQ file.&Input: FASTQ file.
+Output:** FASTQ file plus an HTML file containing statistics on the&Output: FASTQ file plus an HTML file containing statistics on the
+*Figure 2.****** FASTQ file.***&*Figure 2.**FASTQ file.**
+Component:** Hpg-aligner.****&Component:** Hpg-aligner.**
+Input:** VCF&Input:** VCF**
+the corresponding QC and functional annotations.&the corresponding QC and functional annotations.**
+Core features:**&**Core features:**
+Regulatory:**&**Regulatory:**
+Functional annotation**&**Functional annotation**
+Variation**&**Variation**
+Systems biology**&**Systems biology**
+[VNC](../../../salomon/accessing-the-cluster/graphical-user-interface/vnc.html)**.&**[VNC](../../../salomon/accessing-the-cluster/graphical-user-interface/vnc.html)**.
+<!-- -->&
+ id="Key_management" class="mw-headline">&
+Workaround:**&**Workaround:**
+-g** : Generates extra debugging information usable by GDB. -g3&-g** : Generates extra debugging information usable by GDB. -g3**
+-O0** : Suppress all optimizations.&-O0** : Suppress all optimizations.**
diff --git a/source/replace.txt b/source/replace.txt
deleted file mode 100644
index 5eaf20e3..00000000
--- a/source/replace.txt
+++ /dev/null
@@ -1,280 +0,0 @@
- []()&
- **[]()&**
-- - &
-.[]()&.
-### []()[]()&###
-### []()&###
-### **&###
-1. style="text-align: left; float: none; ">Locate and modify&1. Locate and modify
-2000](../uv-2000/@@images/04ce7514-8d27-4cdb-bf0f-45d875c75df0.jpeg "UV 2000")&
-2](../executionaccess2.jpg/@@images/bed3998c-4b82-4b40-83bd-c3528dde2425.jpeg "Execution access 2")&
-2); its mate is mapped to 37 on the reverse strand (32). Read r002 has&
-2. style="text-align: left; float: none; ">&2. Check Putty settings:
-[](7D_Enhanced_hypercube.png)&
-access&
-access](../executionaccess.jpg/@@images/4d6e7cb7-9aa7-419c-9583-6dfd92b2c015.jpeg "Execution access")
-According to FLAG 163 (=1+2+32+128), the read mapped to position 7 is&
-&
-Analyzer](Snmekobrazovky20151204v15.35.12.png/@@images/fb3b3ac2-a88f-4e55-a25e-23f1da2200cb.png "Intel Trace Analyzer")&
-and comes to IT4I (represented by the blue dashed line). The data&
-Anselm](../../anselm-cluster-documentation/Authorization_chain.png "Authorization chain")&
-&
-&
-&
-are mandatory, the rest is optional but strongly recommended. Each line&
-class="anchor-link">&
-class="Apple-converted-space">&
-class="discreet visualHighlight">&
-class="emphasis">&
-class="glossaryItem">&
-class="highlightedSearchTerm">&
-class="highlightedSearchTerm">SSH</span><span>&highlightedSearchTerm
- class="hps">&
-class="hps">&
- class="hps">More</span> <span class="hps">&
-class="hps trans-target-highlight">&
-class="internal-link">&
- class="internal-link"><span id="result_box" class="short_text"><span&
-class="monospace">&
-class="monospace">LAPACKE</span> module, which includes Intel's LAPACKE&LAPACKE modelu, which includes Intel's LAPACKE
- class="n">&
-### class="n">&###
-class="n">&
- class="pre">&
-class="pun">node_group_key&
-class="short_text"><span&
-class="smarterwiki-popup-bubble-body"><span&
-class="smarterwiki-popup-bubble-links-container"><span&
-class="smarterwiki-popup-bubble-links-row">[{.smarterwiki-popup-bubble-link-favicon}](http://maps.google.com/maps?q=HDF5%20icc%20serial%09pthread%09hdf5%2F1.8.13%09%24HDF5_INC%20%24HDF5_SHLIB%09%24HDF5_INC%20%24HDF5_CPP_LIB%09%24HDF5_INC%20%24HDF5_F90_LIB%0A%0AHDF5%20icc%20parallel%20MPI%0A%09pthread%2C%20IntelMPI%09hdf5-parallel%2F1.8.13%09%24HDF5_INC%20%24HDF5_SHLIB%09Not%20supported%09%24HDF5_INC%20%24HDF5_F90_LIB "Search Google Maps"){.smarterwiki-popup-bubble-link}[{.smarterwiki-popup-bubble-link-favicon}](http://www.google.com/search?q=HDF5%20icc%20serial%09pthread%09hdf5%2F1.8.13%09%24HDF5_INC%20%24HDF5_SHLIB%09%24HDF5_INC%20%24HDF5_CPP_LIB%09%24HDF5_INC%20%24HDF5_F90_LIB%0A%0AHDF5%20icc%20parallel%20MPI%0A%09pthread%2C%20IntelMPI%09hdf5-parallel%2F1.8.13%09%24HDF5_INC%20%24HDF5_SHLIB%09Not%20supported%09%24HDF5_INC%20%24HDF5_F90_LIB "Search Google"){.smarterwiki-popup-bubble-link}[](http://www.google.com/search?hl=com&btnI=I'm+Feeling+Lucky&q=HDF5%20icc%20serial%09pthread%09hdf5%2F1.8.13%09%24HDF5_INC%20%24HDF5_SHLIB%09%24HDF5_INC%20%24HDF5_CPP_LIB%09%24HDF5_INC%20%24HDF5_F90_LIB%0A%0AHDF5%20icc%20parallel%20MPI%0A%09pthread%2C%20IntelMPI%09hdf5-parallel%2F1.8.13%09%24HDF5_INC%20%24HDF5_SHLIB%09Not%20supported%09%24HDF5_INC%20%24HDF5_F90_LIB+wikipedia "Search Wikipedia"){.smarterwiki-popup-bubble-link}</span></span></span></span></span>&
-class="smarterwiki-popup-bubble-links"><span&
-class="smarterwiki-popup-bubble smarterwiki-popup-bubble-active smarterwiki-popup-bubble-flipped"><span&&
-class="smarterwiki-popup-bubble-tip"></span><span
-Cluster](https://docs.it4i.cz/salomon/vpn_contacting_https_cluster.png/@@images/22b15d8c-5d5f-4c5c-8973-fbc4e9a32128.png "VPN Contacting Cluster")](../vpn_contacting_https_cluster.png)&
-Cluster](https://docs.it4i.cz/salomon/vpn_contacting_https.png/@@images/ff365499-d07c-4baf-abb8-ce3e15559210.png "VPN Contacting Cluster")](../vpn_contacting_https.png)&
-Cluster](https://docs.it4i.cz/salomon/vpn_contacting.png/@@images/9ccabccf-581a-476a-8c24-ce9842c3e657.png "VPN Contacting Cluster")](../vpn_contacting.png)&&
-column and referenced from the genotype fields as 1-based indexes to&
-component where they can be analysed directly by the user that produced&
-connection](https://docs.it4i.cz/anselm-cluster-documentation/anyconnecticon.jpg/@@images/ebdd0e41-e839-497e-ab33-45162d00b03b.jpeg "Successfull connection")](../../anselm-cluster-documentation/anyconnecticon.jpg)&
-Connection](https://docs.it4i.cz/salomon/vpn_successfull_connection.png/@@images/45537053-a47f-48b2-aacd-3b519d6770e6.png "VPN Succesfull Connection")](../vpn_successfull_connection.png)&&
-Connect](Snmekobrazovky20160211v14.27.45.png/@@images/3550e4ae-2eab-4571-8387-11a112dd6ca8.png "Allinea Reverse Connect")&
-contains a P (padding) operation which correctly aligns the inserted&
-.contenttype-file}&
-[](cygwin-and-x11-forwarding.html)&
-data, the separator indicates whether the data are phased (|) or&
-[{.image-inline width="451"&
-[&
-[&
-file](../instalationfile.jpg/@@images/202d14e9-e2e1-450b-a584-e78c018d6b6a.jpeg "Installation file")&
-filters available. The tool includes a genomic viewer (Genome Maps 30)&
-&
-[](Fluent_Licence_1.jpg)&
-[](Fluent_Licence_2.jpg)&
-[](Fluent_Licence_3.jpg)&
-[](Fluent_Licence_4.jpg)&
-for each sequenced patient. These lists files together with primary and&
- forwarding style="text-align: left; float: none; ">&
-genomic coordinates.](images/fig6.png.1 "fig6.png")&
-genomic position or region. All alternate alleles are listed in the ALT&
-[](gnome-compute-nodes-over-vnc.png)&
-### Gnome on Windows**&### Gnome on Windows
-[](gnome-terminal.png)&
-height="513"}](ddt1.png)&
-[****](TightVNC_login.png)&
- [](PuTTY_host_Salomon.png)&
- [](PuTTY_open_Salomon.png)&
- [](PuTTY_save_Salomon.png)&
-[](totalview1.png)&
-&
-&
- id="Key_management" class="mw-headline">Key management&
-increases.](images/fig5.png.1 "fig5.png")&
-insertion; the third a SNP; the fourth a large structural variant&
-instalation](../successfullinstalation.jpg/@@images/c6d69ffe-da75-4cb6-972a-0cf4c686b6e1.jpeg "Successfull instalation")&
-](../copy_of_vpn_web_install_3.png)&
-Install](https://docs.it4i.cz/salomon/vpn_web_download_2.png/@@images/3358d2ce-fe4d-447b-9e6c-b82285f9796e.png "VPN Install")](../vpn_web_download_2.png)&
-Install](https://docs.it4i.cz/salomon/vpn_web_download.png/@@images/06a88cce-5f51-42d3-8f0a-f615a245beef.png "VPN Install")](../vpn_web_download.png)&
-Install](https://docs.it4i.cz/salomon/vpn_web_install_2.png/@@images/c2baba93-824b-418d-b548-a73af8030320.png "VPN Install")](../vpn_web_install_2.png)[
-Install](https://docs.it4i.cz/salomon/vpn_web_install_4.png/@@images/4cc26b3b-399d-413b-9a6c-82ec47899585.png "VPN Install")](../vpn_web_install_4.png)&
-Install](https://docs.it4i.cz/salomon/vpn_web_login_2.png/@@images/be923364-0175-4099-a363-79229b88e252.png "VPN Install")](../vpn_web_login_2.png)&
-Install](https://docs.it4i.cz/salomon/vpn_web_login.png/@@images/5eac6b9c-22e4-4abe-ab38-e4ccbe87b710.png "VPN Install")](../vpn_web_login.png)&
-&
-login](https://docs.it4i.cz/salomon/vpn_login.png/@@images/5102f29d-93cf-4cfd-8f55-c99c18f196ea.png "VPN login")](../vpn_login.png)&&
-&
-login](../successfullconnection.jpg "successful login")&
-](../../anselm-cluster-documentation/anyconnectcontextmenu.jpg)&&
-mismatches. Read r004 is aligned across an intron, indicated by the N&
-### Notes **&### Notes
-of reference sequences. Notably, r001 is the name of a read pair.&
-of the base before the variant. (b–f ) Alignments and VCF&
-of the body describes variants present in the sampled population at one&
-&
-out.](images/fig1.png "Fig 1")&
-[Pageant (for Windows&
- [](PageantV.png)&
-&
-position of the first aligned base. The CIGAR string for this alignment&
-Preferences](gdmscreensaver.png/@@images/44048cfa-e854-4cb4-902b-c173821c2db1.png "Screensaver Preferences")](../../../../salomon/gnome_screen.jpg.1)&
-pre-processor converts raw data into a list of variants and annotations&
-present in the sequence field. The NM tag gives the number of&
-profile](../loginwithprofile.jpg/@@images/a6fd5f3f-bce4-45c9-85e1-8d93c6395eee.jpeg "Login with profile")&
-PuTTY - class="Apple-converted-space"> before we start SSH connection ssh-connection style="text-align: start; "}&
-[](PuttyKeygenerator_001V.png)&
- [](PuttyKeygenerator_002V.png)&
- [](20150312_143443.png)&
- [](PuttyKeygenerator_004V.png)&
- [](PuttyKeygenerator_005V.png)&
- [](PuttyKeygenerator_006V.png)&
- [](PuttyKeygeneratorV.png)&
- [](PuTTY_keyV.png)&
-reference bases replaced by the haplotype in the ALT column. The&
-&
-&
-&
-&
-&
-&
-representations of different sequence variants: SNP, insertion,&
-resources on&
-&
-Rstudio&Rstudio**
-&
-[](../salomon-2)&
-[](salomon)&
-[](salomon)&
-&
-&
-&![]](salomon-3.jpeg)
-&
-](gdmdisablescreensaver.png)&
-[](vtune-amplifier)&
-Screenshot](Snmekobrazovky20141204v12.56.36.png "CUBE Screenshot")&
-&
-secondary (alignment) data files are stored in IT4I sequence DB and&
-sequences. Padding operations can be absent when an aligner does not&
-session](../../../../salomon/gnome_screen.jpg/@@images/7758b792-24eb-48dc-bf72-618cda100fda.png "Default Gnome session")](https://docs.it4i.cz/get-started-with-it4innovations/gnome_screen.jpg)&
-shows an example of a deletion (present in SAMPLE1) and a replacement of&
-</span>&
-<span&
- <span&
- [<span class="anchor-link">&
-<span class="discreet">&
-<span class="discreet"></span>&
-<span class="glossaryItem">&
- <span class="glossaryItem">&
-<span class="hps">&
-<span class="hps alt-edited">&
-<span class="listitem">&
-<span class="n">&
-<span class="s1">&
- <span class="WYSIWYG_LINK">&
-<span dir="auto">&
-<span id="__caret">&
-<span id="__caret"><span id="__caret"></span></span>&
-(<span id="result_box">&
-<span id="result_box" class="short_text"><span class="hps">&
- <span id="result_box"><span class="hps">&
-</span></span>&
-</span> <span&
-<span><span>&
-</span> <span class="hps">&
- </span> <span class="hps">&
-</span> <span class="hps">who have a valid</span> <span&
-<span><span class="monospace">&
-<span><span>Introduction&###Introduction
-</span></span><span><span>&
-</span></span></span></span><span><span>&
-</span></span><span><span><span><span>&
-.<span style="text-align: left; "> </span>&
-<span style="text-align: start; ">&
-{.state-missing-value
- style="text-align: left; float: none; ">&
- style="text-align: left; float: none; ">&
- style="text-align: left; float: none; ">change it&change it to
- style="text-align: left; float: none; ">Check Putty settings:&
- style="text-align: left; float: none; ">Enable X11&Enable X11
- style="text-align: left; float: none; "> &
-style="text-align: start; ">&
-style="text-align: start; float: none; ">&
-&
-**Summary&**Summary**
-support multiple sequence alignment. The last six bases of read r003 map&
-Tape Library T950B**&**Tape Library T950B**
-.text}.&
-.text}&
-that enables the representation of the variants in the corresponding&
-]&![]
-to position 9, and the first five to position 29 on the reverse strand.&
- to</span>&
-[](totalview2.png)&
-tunnel](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/putty-tunnel.png/@@images/4c66cd51-c858-473b-98c2-8d901aea7118.png "PuTTY Tunnel")](putty-tunnel.png)&
-two bases by another base (SAMPLE2); the second line shows a SNP and an&
-unphased (/). Thus, the two alleles C and G at the positions 2 and 5 in&
-uploaded to the discovery (candidate priorization) or diagnostic&
-users)](putty/PageantV.png)&
-use simplest representation possible and lowest coordinate in cases&
-&
-&
-vncviewer](../../../../anselm-cluster-documentation/vncviewer.png/@@images/bb4cedff-4cb6-402b-ac79-039186fe5df3.png "Vncviewer")&
-[&
-Workflow](virtualization-job-workflow "Virtualization Job Workflow")&
- &
-[]() &
- &
- [**](TightVNC_login.png)&
-[](gnome-terminal.png)&
-[](gnome-compute-nodes-over-vnc.png)&
-screensaver](https://docs.it4i.cz/get-started-with-it4innovations/ing-the-clusters/graphical-user-interface/vnc/gdmdisablescreensaver.png/@@images/8a4758d9-3027-4ce4-9a90-2d5e88197451.png "Disable lock screen and screensaver")](gdmdisablescreensaver.png)&
--
GitLab